PathBench-MILPathBench-MIL is a comprehensive, flexible benchmarking/AutoML framework for multiple instance learning in histopathology. PathBench-MIL is expected to be deprecated and replaced by PathForge.https://github.com/Sbrussee/PathBench-MILPathBench-MILbiotools:PathBench-MILhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3474Machine learningLinuxShellPythonGPL-3.0LegacyFree of chargehttp://edamontology.org/operation_2425Optimisation and refinementhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_2990Classificationhttp://edamontology.org/data_2093Data referencehttp://edamontology.org/format_3752CSVhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFpathforgehasNewVersion10.48550/arXiv.2512.17517BaktaRapid & standardized annotation of bacterial genomes, MAGs & plasmidshttps://github.com/oschwengers/baktabaktabiotools:baktav1.12.1Command-line toolWeb applicationhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0091BioinformaticsLinuxMacPythonGPL-3.0MatureFree of chargeOpen accessToolsGermanyhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2914Sequence features metadatahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/format_1975GFF3http://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/format_3329HMMER3bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fastahttps://github.com/oschwengers/baktaRepositoryhttps://github.com/oschwengers/bakta/issuesIssue trackerhttps://bioconda.github.io/recipes/bakta/README.htmlOtherhttps://bakta.computational.bioServicehttps://zenodo.org/records/14916843OtherMandatory annotation databasev6.0https://github.com/oschwengers/bakta/blob/main/README.mdGeneralhttps://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.mdContributions policyhttps://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.mdCode of conducthttps://bakta.readthedocs.io/User manualdiamonduseshmmer3usesinfernalusestrnascan-seusesblastusesaragornusespilercruses10.1099/mgen.0.00068534739369PMC8743544Primary1.110.1093/nar/gkaf33540271661PMC12230652PrimaryOliver Schwengersoliver.schwengers@cb.jlug.dehttps://github.com/oschwengershttps://orcid.org/0000-0003-4216-2721PersonPrimary contactDeveloperMaintainerJustus Liebig University Giessenhttps://www.uni-giessen.deInstituteProviderBIOSZENBIOSZEN is an open-source R package and modular Shiny application for reproducible analysis and visualization of experimental biological data from Excel or CSV files. It supports statistical testing, control-based normalization, replicate-aware quality control, and customizable scientific plots.
Its microbial growth-curve module analyzes optical-density time series and automatically extracts quantitative growth parameters, including maximum specific growth rate (µMax), doubling time, lag time, maximum optical density (ODmax), time to maximum growth, area under the curve (AUC), and initial optical density (OD0).
Results can be exported as processed datasets, statistical summaries, analysis metadata, scientific graphics, and editable PowerPoint figures.https://github.com/bioszen/BIOSZENbioszenbiotools:bioszen2.1.1Desktop applicationWeb applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3301MicrobiologyWindowsMacRGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_0337VisualisationStatistical analysis, control-based normalization, replicate-aware quality control, and customizable visualization of experimental biological data from Excel or CSV files.http://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2945Data analysishttp://edamontology.org/operation_0337VisualisationAnalysis and visualization of microbial optical-density time series, including extraction of uMax, max_percap_time, doubling time, lag time, ODmax, max_time, AUC, OD0, and related growth parameters.https://github.com/bioszen/BIOSZENRepositorySource code, example files, documentation, and development history.https://github.com/bioszen/BIOSZEN/issuesIssue trackerBug reports, installation problems, and feature suggestions.https://bioszen-test.share.connect.posit.cloudServiceLimited online demonstration of the BIOSZEN Shiny application.https://zenodo.org/records/18217210Downloads pageArchived release files and permanent software record.2.1.1https://bioszen.r-universe.dev/BIOSZENSoftware packageInstallable R package for BIOSZEN 2.1.1, including access to the Shiny application.2.1.1https://github.com/bioszen/BIOSZEN#readmeGeneralUser manualQuick start guidehttps://github.com/bioszen/BIOSZEN/blob/main/inst/app/www/MANUAL_EN.mdUser manualComplete BIOSZEN user manual in English.https://github.com/bioszen/BIOSZEN#citationCitation instructions10.5281/zenodo.18217210Primaryall versions10.5281/zenodo.18217522Primary1.0.0Benjamín Szenfeldbioszenf@gmail.comhttps://orcid.org/0009-0003-4702-4149PersonDeveloperMaintainerPrimary contactRNATrackerPrediction of mRNA subcellular localization using deep recurrent neural networks | RNATracker is a deep learning approach to learn mRNA subcellular localization patterns and to infer its outcome. It operates on the cDNA of the longest isoformic protein-coding transcript of a gene with or without its corresponding secondary structure annnotations. The learning targets are fractions/percentage of the transcripts being localized to a fixed set of subcellular compartments of interesthttps://www.github.com/HarveyYan/RNATrackerRNATrackerbiotools:RNATrackerhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0203Gene expressionPythonGPL-3.0http://edamontology.org/operation_2489Subcellular localisation predictionhttp://edamontology.org/operation_0443trans-regulatory element prediction10.1093/BIOINFORMATICS/BTZ33731510698PMC6612824Mathieu Blanchetteblanchem@cs.mcgill.caPersonCSP-AnalyzerA novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening.
A fast and efficient multi-spectrum anlayzer for 2-D NMR Fragment Screening based on SMOTE-ENN machine-learning discriminator. - rubbs14/CSP-Analyzer.https://github.com/rubbs14/CSP-Analyzer/releases/tag/v1.0csp-analyzerbiotools:csp-analyzerCommand-line toolhttp://edamontology.org/topic_0593NMRhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3336Drug discoveryC#PythonGPL-3.0http://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_3860Spectrum calculation10.1016/J.CSBJ.2020.02.01532257044PMC7096735G.M. Popowiczgrzegorz.popowicz@helmholtz-muenchen.dePersonClustVisWeb tool which allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps. Data can be uploaded as a file or by copy-pasteing it to the text box.http://biit.cs.ut.ee/clustvisclustvisbiotools:clustvis1RRID:SCR_017133rridWeb applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_2269Statistics and probabilityLinuxWindowsMacRGPL-3.0Elixir-EEFree of chargeToolsEstoniahttp://edamontology.org/operation_0313Gene expression clusteringhttp://edamontology.org/operation_2942Treemap visualisationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2939Principal component plottinghttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/data_3111Processed microarray datahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_3113Sample annotationhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_0928Gene expression profilehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix formathttps://github.com/taunometsalu/ClustVisRepositoryA code repository in github.https://hub.docker.com/r/taunometsalu/clustvis/Container fileDocker imagehttps://biit.cs.ut.ee/clustvis/General10.1093/nar/gkv46825969447PMC4489295PrimaryELIXIR-EEInstituteProviderTauno Metsalutauno.metsalu@ut.eePersonPrimary contactbiit.support@ut.eePersonPrimary contactMOODSA suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds. MOODS can also process high-order PWMs with dependencies between adjacent positions and sequence variants such as SNPs, insertions and deletions.https://www.cs.helsinki.fi/group/pssmfind/moodsbiotools:moodsCommand-line toolScripthttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0157Sequence composition, complexity and repeatsLinuxC++PythonGPL-3.0Animal and Crop Genomicshttp://edamontology.org/operation_0239Sequence motif recognitionhttps://github.com/jhkorhonen/MOODSRepositoryhttps://github.com/jhkorhonen/MOODS/issuesIssue trackerhttps://github.com/jhkorhonen/MOODS/wiki/Getting-startedGeneral10.1109/tcbb.2009.3521071798Primary10.1093/bioinformatics/btw68328011774Primary10.1093/bioinformatics/btp55419773334PMC2778336Primaryjanne.h.korhonen@aalto.fiPersonPrimary contactPangolinPangolin is a deep-learning based method for predicting splice site strengths (for details, see Zeng and Li, Genome Biology 2022). It is available as a command-line tool that can be run on a VCF or CSV file containing variants of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences.https://github.com/tkzeng/Pangolinpangolinbiotools:pangolinCommand-line toolhttp://edamontology.org/topic_3320RNA splicinghttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3676Exome sequencingMacLinuxWindowsPythonGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_0232Sequence merginghttp://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_3752CSV10.1186/s13059-022-02664-435449021PMC9022248Yang I Liyangili1@uchicago.eduhttps://orcid.org/0000-0002-0736-251XPersonTony ZengkMetaShotThe application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting.https://github.com/gdefazio/kMetaShotkMetaShotbiotools:kMetaShotCommand-line toolhttp://edamontology.org/topic_3174MetagenomicsLinuxPythonGPL-3.0EmergingFree of chargeOpen accessToolsMarine MetagenomicsItalyhttps://github.com/gdefazio/kMetaShotOther10.1093/bib/bbae680Giuseppe Defaziogiuseppe.defazio@uniba.ithttps://persone.ict.uniba.it/rubrica/@@cerca?advanced_search=False&sort_on=&SearchableText=defaziohttps://orcid.org/0000-0002-9356-5224PersonDeveloperPost-Doc Researcher at University of Barimtagmtag is a Python-based command line tool for jointly analyzing multiple sets of GWAS summary statistics as described by Turley et. al. (2018). It can also be used as a tool to meta-analyze GWAS results.https://github.com/JonJala/mtagmtagbiotools:mtag0.9.0Command-line toolhttp://edamontology.org/topic_3517GWAS studyPerlPythonRGPL-3.0Maturehttp://edamontology.org/operation_3209Genome comparisonhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttps://github.com/JonJala/mtag/wikiGeneral10.1038/s41588-017-0009-429292387PMC5805593PrimarymothurOpen-source, platform-independent, community-supported software for describing and comparing microbial communitieshttp://mothur.org/mothurbiotools:mothurSuitehttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0084PhylogenyC++GPL-3.0http://edamontology.org/operation_3200DNA barcodinghttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3921Sequence read processinghttp://edamontology.org/operation_0324Phylogenetic analysishttps://github.com/mothur/mothurRepositoryhttps://github.com/mothurOtherRepositorymothur GitHub organizationhttp://mothur.org/wiki/mothur_manual/User manualhttp://mothur.org/wiki/Othermothur Wiki page10.1128/aem.01541-0919801464PMC2786419thromboSeqthromboSeq is a bioinformatics tool designed for the analysis of thrombosis-related sequencing data, providing functionalities for variant calling, annotation, and functional interpretation. It streamlines the processing of high-throughput sequencing data to identify genetic variants associated with thrombotic disorders.https://github.com/MyronBest/thromboSeq_source_codethromboseqbiotools:thromboseqShellRPerlGPL-3.0Maturehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_2058Gene expression report format10.3390/cancers1318464434572871PMC8468408Primaryqamqam is a Python library and command-line tool to compute 3D surface-distances for evaluating liver ablation/tumor completeness based on segmentation images.https://github.com/artorg-unibe-ch/qamqambiotools:qamCommand-line toolLibraryWorkflowhttp://edamontology.org/topic_3384Medical imagingPythonGPL-3.0Maturehttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3438Calculationhttp://edamontology.org/data_2968Image10.3389/fonc.2021.62309833777768PMC7988092PrimaryPanAbyssPanAbyss is a tool for exploring and visualizing pangenome graphs. It allows users to search for and display regions of a pangenome using coordinates on a reference individual or based on annotations. It also enables searching for regions associated with a selected set of individuals (for example, those linked to a phenotype), computing proximity trees, and retrieving sequences from a given region.https://github.com/Pange31/PanAbysspanabyssbiotools:panabyss1.4.0Web applicationhttp://edamontology.org/topic_0080Sequence analysisWindowsMacLinuxGPL-3.0EmergingFree of chargeOpen accessFrancehttps://github.com/Pange31/PanAbyss/wikiGeneralGrazianifabien.graziani@inrae.frhttps://orcid.org/0009-0002-3966-0906InstitutePrimary contactmetagWGSmetagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.https://forge.inrae.fr/genotoul-bioinfo/metagwgsmetagwgsbiotools:metagwgs2.32.5.02.6.0Workflowhttp://edamontology.org/topic_3174MetagenomicsLinuxPythonGPL-3.0MatureFree of chargeOpen accessFrancehttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttps://forge.inrae.fr/genotoul-bioinfo/metagwgsRepositorySee documentation, source code and functionnal test documentation.https://forge.inrae.fr/genotoul-bioinfo/metagwgs-test-datasetsTest dataFunctional tests data and scripthttps://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.htmlUser manualWe provide up to date installation documentation, usage documentation, output description and functionnal test datasets and procedure.10.1101/2024.09.13.612854PreprintmetagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads
Jean Mainguy, Maïna Vienne, Joanna Fourquet, Vincent Darbot, Céline Noirot, Adrien Castinel, Sylvie Combes, Christine Gaspin, Denis Milan, Cécile Donnadieu, Carole Iampietro, Olivier Bouchez, Géraldine Pascal, Claire Hoede
bioRxiv 2024.09.13.612854Claire Hoedeclaire.hoede@inrae.frhttps://orcid.org/0000-0001-5054-7731PersonPrimary contactGenoToul bioinformatics facilityhttp://bioinfo.genotoul.fr/DivisionProviderbinchickenBin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassemblyhttps://aroneys.github.io/binchickenbinchickenbiotools:binchickenv0.13.5Command-line toolhttp://edamontology.org/topic_3174MetagenomicsLinuxShellPythonRGPL-3.0Maturehttp://edamontology.org/operation_3730Cross-assemblyhttp://edamontology.org/operation_3798Read binninghttps://aroneys.github.io/binchickenGeneral10.1038/s41592-025-02901-141233543Method10.1038/s41587-025-02738-140670710PrimaryBin Chicken is built on the SingleM tool, described in this publication.gff3sortGFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix toolshttps://github.com/tao-bioinfo/gff3sortgff3sortbiotools:gff3sortv1.0.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyLinuxPerlGPL-3.0MatureFree of chargehttp://edamontology.org/operation_3802Data sortinghttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_1975GFF3gff3sort.pl [input GFF3 file] >output.sort.gff310.1186/s12859-017-1930-329137598PMC5686826CLIFinderCLIFinder is a Galaxy tool designed to identify potential L1 Chimeric Transcripts from RNA-seq data by analyzing paired-end reads in the human genome. It allows customization to detect transcripts initiated by different repeat elements.https://github.com/GReD-Clermont/CLIFinderCLIFinderbiotools:CLIFinder0.5.2ScriptCommand-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308TranscriptomicsRPerlGPL-3.0Galaxy ToolsGalaxyEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_2403Sequence analysishttps://github.com/GReD-Clermont/CLIFinder/Repositoryhttps://toolshed.g2.bx.psu.edu/repository?repository_id=5c73d1cf20ab37c3Galaxy servicehttps://github.com/GReD-Clermont/CLIFinder/blob/main/README.rstAPI documentationhttps://github.com/GReD-Clermont/CLIFinder/#usageCommand-line options10.1093/bioinformatics/btx67129069308Primarysnp-distsPairwise SNP distance matrix from a FASTA sequence alignmenthttps://github.com/tseemann/snp-distssnp-distsbiotools:snp-distsv1.2.0Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0080Sequence analysisCShellGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0260Sequence alignment conversionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTATorsten SeemannPersonFabian KlötzlPersonAndrew J PagePersonNanofiltFiltering and trimming of long read sequencing data.http://nanoplot.bioinf.benanofiltbiotools:nanofiltCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3168SequencingPythonGPL-3.0LegacyOpen accesshttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttps://github.com/wdecoster/nanofiltRepository10.1093/BIOINFORMATICS/BTY14929547981PMC6061794Wouter De Costerwouter.decoster@molgen.vib-ua.behttps://orcid.org/0000-0002-5248-8197PersonVerityMapVerityMap is a tool for mapping long reads to assemblies of extra-long tandem repeats, producing SAM files and identifying potential heterozygous sites and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and ONT reads and generates interactive HTML plots for variant analysis.https://github.com/ablab/VerityMapVerityMapbiotools:VerityMaphttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622GenomicsCCUDAPythonC++GPL-3.0Maturehttp://edamontology.org/operation_0523Mapping assemblyhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/ablab/tandemQUAST/issuesIssue tracker10.1093/bioinformatics/btaa44032657355PMC7355294Porechopadapter trimmer for Oxford Nanopore readshttps://github.com/rrwick/PorechopPorechopbiotools:Porechopv0.2.4CPythonC++GPL-3.0Legacyhttp://edamontology.org/operation_2121Sequence file editinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQalphapickleAlphaPickle is a Python tool that converts AlphaFold and ColabFold output files into user-friendly CSV files and plots, enabling easy analysis and visualization of protein prediction data without requiring programming expertise. It processes .pkl, .json, and PDB files to extract and visualize metrics like pLDDT and PAE.https://github.com/mattarnoldbio/alphapicklealphapicklebiotools:alphapicklev1.4.1PythonGPL-3.0Maturehttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_2085Structure reporthttp://edamontology.org/format_3464JSONMetaProteomeAnalyzer-CloudThe MetaProteomeAnalyzer Cloud (MPA Cloud) is an intuitive, open-source tool for metaproteomics data analysis and interpretation, designed to analyse comprehensive metaproteomics data from tandem mass spectrometry experiments through a web interface.https://mdoa-tools.bi.denbi.de/mpacloud/mpa-cloudbiotools:mpa-cloudWeb servicehttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_4060Metaproteomicshttp://edamontology.org/topic_0121ProteomicsJavaTypeScriptGPL-3.0MatureFree of chargeOpen accessGermanyhttps://gitlab.com/mdoa-group/mpa-websiteRepositoryhttps://gitlab.com/mdoa-group/mpa-cloud-serverRepositoryhttps://mdoa-tools.bi.denbi.de/mpacloud/documentationUser manualmetaproteomeanalyzerisNewVersionOfmpa_portableisNewVersionOf10.1038/s41596-020-0368-73285998410.3389/fmicb.2019.0188331474963PMC670742510.1021/acs.analchem.7b0354429215871PMC575722010.1021/pr501246w25660940Kay SchallertDaniel KautznerBenjamin J. SaalfeldProf. Dr.-Ing. Robert HeyerLudwig KnocheMalte BöttcherinfluentialA comprehensive R package for identifying and ranking influential nodes in biological and other complex networks. The package implements the Integrated Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR), SIRIR, and numerous network centrality measures, enabling network topology analysis, influential node detection, feature prioritization, and candidate biomarker discovery. It also provides functions for network reconstruction, centrality assessment, visualization, and analysis of relationships between centrality measures.https://asalavaty.github.io/influential/influentialbiotools:influentialLibraryhttp://edamontology.org/topic_3307Computational biologyLinuxWindowsMacRGPL-3.0Maturehttp://edamontology.org/operation_2495Expression analysishttp://edamontology.org/operation_3927Network analysisIdentification of influential nodes
Network centrality analysis
Feature prioritization and ranking
Network reconstruction
Biomarker candidate discovery
Topological network analysis
Integrative rankingivi()
exir()https://github.com/asalavaty/influentialRepositorySource codehttps://asalavaty.github.io/influential/OtherDocumentationhttps://github.com/asalavaty/influentialDownloads pagehttps://cran.r-project.org/package=influentialDownloads pageCRAN Versionhttps://asalavaty.github.io/influential/articles/Vignettes.htmlUser manual10.1016/j.patter.2020.10005233205118PMC7660386PrimarySNP-sitesFinds SNP sites from a multi-FASTA alignment file.https://sanger-pathogens.github.io/snp-sites/snp-sitesbiotools:snp-sites2.5.1Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_2885DNA polymorphismLinuxCGPL-3.0Open accesshttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3820Relaxed PHYLIP Sequentialhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3016VCFsnp-sites my_alignment.aln
snp-sites my_gzipped_alignment.aln.gzhttps://github.com/sanger-pathogens/snp-sitesRepositoryhttps://sanger-pathogens.github.io/snp-sites/General10.1099/mgen.0.00005628348851PMC5320690PrimaryParseSNPA small <720Kb C++ windows utility. That allows you to load Ancestry, 23andMe, FTDNA, or Genes for Good RAW DNA files search them, merge them. covert them to Ancestry format. But also create files from peer reviewed publications to compare with you loaded data to give your genetic disposition for the condition you have entered the data for an statistical risk if OR values are included. Included with the program are example files for Type 2 Diabetes risk factors. (As I have type 2 Diabetes so I could test the results).https://britrobin.github.io/ParseSNP/parsesnp21-26biotools:parsesnp21-261.1.1Desktop applicationhttp://edamontology.org/topic_3577Personalised medicineWindowsC++GPL-3.0EmergingFree of chargeOpen accesshttps://britrobin.github.io/ParseSNP/OtherGit page for easy installer and pdf manual downloadhttps://github.com/BritRobin/ParseSNPRepositoryGitHub repositoryhttps://britrobin.github.io/ParseSNP/Software packageWindows x64 or x86 installer1.1.1https://raw.githubusercontent.com/BritRobin/ParseSNP/master/ParseSNP_Manual.pdfUser manualpdf user manualCompuCell3DCompuCell3D is a multiscale multicellular virtual tissue modeling and simulation environment. CompuCell3D is written in C++ and provides Python bindings for model and simulation development in Python.https://compucell3d.org/SrcBincompucell3dbiotools:compucell3d4.8.0Command-line toolhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_3307Computational biologyWindowsLinuxMacPythonC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_2426Modelling and simulationhttps://compucell3d.org/SrcBinRepositoryhttps://www.reddit.com/r/CompuCell3D/Discussion forumhttps://compucell3d.org/API documentationhttps://compucell3d.org/TutorialsTraining materialhttps://compucell3d.org/PublicationsCitation instructions10.1016/b978-0-12-388403-9.00013-822482955PMC3612985PrimaryNuclearPhaserNuclearPhaser is a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline for dikaryons.https://github.com/JanaSperschneider/NuclearPhasernuclearphaserbiotools:nuclearphaser1.1Scripthttp://edamontology.org/topic_0622GenomicsLinuxMacPythonGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttps://github.com/JanaSperschneider/NuclearPhaserRepositoryhttps://github.com/JanaSperschneider/NuclearPhaser/blob/main/README.mdQuick start guideJana Sperschneiderhttps://github.com/JanaSperschneiderGenErodeWorkflow for whole genome sequencing analysis, including patterns of genome erosion. Written in Snakemake workflow language.https://github.com/NBISweden/GenErodegenerodebiotools:generodeWorkflowhttp://edamontology.org/topic_0622GenomicsOtherGPL-3.0Maturehttp://edamontology.org/operation_0368Sequence maskinghttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2572BAMhttps://github.com/NBISweden/GenErodeGeneralhttps://github.com/NBISweden/GenErode/wikiUser manual10.1186/s12859-022-04757-035698034PMC9195343MethodbiokangaBioKanga is an integrated toolkit of high performance bioinformatics subprocesses targeting the challenges of next generation sequencing analytics. Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.https://github.com/csiro-crop-informatics/biokangabiokangabiotools:biokanga4.4.2Suitehttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0196Sequence assemblyWindowsLinuxMacC++GPL-3.0EmergingFree of chargehttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_3218Sequencing quality controlPicoporeReduce the size of Oxford Nanopore Technologies' datasets without losing information.https://github.com/scottgigante/picoporepicoporebiotools:picopore1.2.0Libraryhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0622GenomicsWindowsLinuxMacPythonGPL-3.0BiocondaPython Software Foundationhttps://anaconda.org/bioconda/picoporeRepositoryBioconda packagehttps://pypi.org/project/picopore/RepositoryPython Software Foundation10.12688/f1000research.11022.1PrimaryScott GigantePersonPrimary contactSLiMEvolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment.https://messerlab.org/slim/SLiM_softwarebiotools:SLiM_software5.2Command-line toolDesktop applicationhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3299Evolutionary biologyWindowsLinuxMacC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0230Sequence generationhttp://edamontology.org/operation_0550DNA substitution modellinghttp://edamontology.org/operation_3946Ecological modellingRun individual-based eco-evolutionary simulations with explicit geneticshttps://messerlab.org/slim/Software catalogueSLiM home page in the Messer Lab websitehttps://github.com/MesserLab/SLiMRepositoryGitHub repository for SLiMhttps://groups.google.com/g/slim-discussDiscussion forumDiscussion forum for SLiM questionshttps://groups.google.com/g/slim-announceMailing listAnnouncements mailing listhttp://benhaller.com/slim/SLiM.zipSource codeA source archive for the command-line `slim` tool only. Complete source code is on GitHub, but most platforms have an installer anyway; see the manual, chapter 2, for installation instructions.https://github.com/MesserLab/SLiM/releases/latestDownloads pageThe GitHub page for the current release version, to obtain full source code.http://benhaller.com/slim/SLiM_Manual.pdfUser manualThe manual for SLiM itselfhttp://benhaller.com/slim/Eidos_Manual.pdfUser manualThe manual for Eidos, the scripting language used by SLiMhttp://benhaller.com/slim/SLiMEidosRefSheets.zipQuick start guideQuick reference sheets for SLiM and Eidos10.1093/molbev/msy22830517680PMC6389312Primary3.0B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.10.1093/molbev/msy23730590560PMC6501880Method3.0B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109.10.1111/1755-0998.1296830565882PMC6393187Primary3.0B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.10.1101/2025.08.07.66915540832315PMC12363870Primary5.0BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes. bioRxiv, 2025.08. 07.66915510.1086/72360137130229PMC10793872Primary4.0B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist 201(5), E127–E139.Philipp Messermesser@cornell.eduhttps://messerlab.orghttps://orcid.org/0000-0001-8453-9377PersonPrimary contactBenjamin C. Hallerbhaller@benhaller.comhttp://benhaller.comhttps://orcid.org/0000-0003-1874-8327PersonPrimary contactPROVEANA software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.http://provean.jcvi.org/index.phpproveanbiotools:proveanWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3120Protein variantsLinuxWindowsMacShellGPL-3.0Animal and Crop Genomicshttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_3197Genetic variation analysishttp://provean.jcvi.org/index.phpGeneral10.1371/journal.pone.004668823056405PMC3466303Primaryhttp://provean.jcvi.org/contact.phpPersonPrimary contactquacQuaC is a snakemake-based pipeline that runs several QC tools for WGS/WES samples and then summarizes their results using pre-defined, configurable QC thresholds.https://github.com/uab-cgds-worthey/quacquacbiotools:quac2.0Command-line toolhttp://edamontology.org/topic_0080Sequence analysisPythonGPL-3.0SequencingMatureFree of chargeOpen accesshttp://edamontology.org/operation_3218Sequencing quality controlhttps://github.com/uab-cgds-worthey/quacRepositoryhttps://github.com/uab-cgds-worthey/quac/releases/tag/2.0Source code2.0https://quac.readthedocs.io/General10.21105/joss.05313Manavalan Gajapathyhttps://github.com/ManavalanGhttps://orcid.org/0000-0002-8606-0113PersonPrimary contactRosalutionRosalution assists researchers study genetic variation 🧬 in patients 🧑🏾🤝🧑🏼 by helping select candidate animal models 🐀🐁🐠🪱 to replicate the variation to further research to derive, diagnose, and provide therapies for ultra-rare diseases. Developed by the UAB Center for Computational Genomics and Data Science (CGDS).https://github.com/uab-cgds-worthey/rosalutionrosalutionbiotools:rosalution0.8.8-erWeb applicationhttp://edamontology.org/topic_0199Genetic variationJavaScriptPythonGPL-3.0Rare DiseaseMatureFree of chargehttps://github.com/uab-cgds-worthey/rosalutionRepositoryhttps://github.com/uab-cgds-worthey/rosalution/issuesIssue trackerhttps://github.com/uab-cgds-worthey/rosalution/releases/tag/0.8.8-erSource code0.8.8-er10.21105/joss.05443Angelina Uno-Antonisonhttps://github.com/SeriousHorncatbio.toolsThe community registry of computational tools and data resources for biosciences.https://bio.toolsbio.toolsbiotools:bio.toolsRRID:SCR_014695rridWeb APIDatabase portalWeb applicationhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0219Data curation and archivalhttp://edamontology.org/topic_3307Computational biologyJavaScriptPythonGPL-3.0EmergingFree of chargeOpen accessToolsDenmarkhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_3671Texthttp://edamontology.org/format_1964plain text format (unformatted)https://biotools.readthedocs.io/en/latest/support.html?highlight=helpHelpdeskhttps://github.com/bio-tools/biotoolsregistry/issuesIssue trackerhttps://biotools.readthedocs.io/en/latest/contributors_guide.html#mailing-listMailing listhttps://github.com/bio-tools/biotoolsregistry/Repositoryhttps://github.com/bio-tools/biotoolsRegistrySource codehttps://biotools.readthedocs.io/en/latest/api_usage_guide.htmlAPI documentationAPI usage guidehttps://biotools.readthedocs.io/en/latest/api_reference.htmlAPI documentationAPI Referencehttps://biotools.readthedocs.io/en/latest/publications.html#citationCitation instructionshttps://biotools.readthedocs.io/en/latest/contributors_guide.htmlContributions policyhttps://biotools.readthedocs.io/en/latest/Generalhttps://biotools.readthedocs.io/en/latest/governance.htmlGovernancehttps://biotools.readthedocs.io/en/latest/curators_guide.htmlUser manualCurators Guide10.1093/nar/gkv1116Primary10.12688/f1000research.12974.1Other10.1093/gigascience/gix022Other10.1007/s10009-015-0392-zOtherContributorshttps://biotools.readthedocs.io/en/latest/contributors.htmlPersonRhizoVision ExplorerRhizoVision Explorer is free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera. Root images are expected to have a high contrast of roots with the background, homogenous lighting, and minimal overlapping of roots.https://github.com/noble-research-institute/RhizoVisionExplorerrhizovision-explorerbiotools:rhizovision-explorerDesktop applicationhttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3298PhenomicsC++GPL-3.0http://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3937Feature extractionhttps://github.com/rootphenomicslab/RhizoVisionExplorer/issuesIssue tracker10.1093/aobpla/plab05634804466PMC8598384PrimaryLarry M. Yorklmyork@noble.orghttps://orcid.org/0000-0002-1995-9479PersonPrimary contactFreezing-PointFreezing-Point is a user-friendly open-source software for the automated analysis of freezing behavior in rodents. Based on recorded videos or pose estimation files. An adaptive, data-driven algorithm automatically determines freezing detection thresholds, reducing subjective bias while preserving user oversight. Freezing-Point adopts a user-oriented design centered on a graphical interface that provides continuous visual access to original data, processing steps and analysis results. This design enables users to inspect, validate or refine results while minimizing unnecessary data manipulation.https://github.com/gillescourtand/Freezing-PointFreezing-Pointbiotools:Freezing-Point1.0.2Desktop applicationhttp://edamontology.org/topic_3304NeurobiologyMacLinuxWindowsPythonGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2425Optimisation and refinementhttps://github.com/gillescourtand/Freezing-Point/releasesBinaries1.0.2https://github.com/gillescourtand/Freezing-Point/blob/main/Doc/User_guide.mdQuick start guideWEBnmaWEBnm@ provides quick, automated computation and analysis of low-frequency normal modes for protein structures.http://apps.cbu.uib.no/webnmawebnmabiotools:webnma3.5Web APISuitehttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0736Protein folds and structural domainsLinuxWindowsMacPythonGPL-3.0BiB toolsCBU toolsUiB toolsELIXIR-NOELIXIR-NorwayMatureFree of chargeOpen access3D-BioInfoNorwayhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0244Protein flexibility and motion analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBConstructs elastic network model from alpha carbon coordinates of the protein, and computes properties to describe large scale conformations. Computes normal modes, fluctuation profiles, inter-residue correlations, conformational overlap analysis and vector field representations. Structural amino acid profiles, and normal mode characteristics describing protein motion, visualized in plots and decorated structure visualizations. White space delimited tabular data for normal modes and the provided plotshttp://edamontology.org/operation_2487Protein structure comparisonhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBPerforms comparative analysis of the normal modes of protein structures. Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins to be compared. Multiple protein structures Heatmaps, dendrograms and structural amino acid profiles for visual comparison of structural similarity. White space delimited tabular data for the provided plotshttps://github.com/reuter-group/webnma3RepositoryIssue trackerhttps://elixir.no/helpdeskHelpdeskHelpdesk and support for ELIXIR Norway services.http://apps.cbu.uib.no/webnma3/howto/singleQuick start guidehttp://apps.cbu.uib.no/webnma3/qandaFAQhttp://apps.cbu.uib.no/webnma3/aboutGeneralCitation instructionsnumpyusesbiopythonusesmatplotlibusesmustangusesdsspuses10.1186/s12859-014-0427-625547242PMC4339738Primary2.010.1186/1471-2105-6-5215762993PMC1274249Primary1.0Nathalie ReuterNathalie.Reuter@uib.nohttp://www.cbu.uib.no/reuter/https://orcid.org/0000-0002-3649-7675PersonPrimary contactDeveloperSandhya P Tiwarihttps://orcid.org/0000-0002-0747-3826PersonDeveloperKidane M TeklePersonDeveloperTristan CragnoliniPersonDeveloperSvenn H GrindhaugPersonDeveloperLars SkjærvenPersonDeveloperGisle SalensmindePersonDeveloperEdvin FuglebakkPersonDeveloperSiv M HollupPersonDeveloperDepartment of Molecular Biology, University of Bergen, NorwayInstituteProviderComputational Biology Unit, Department of Informatics, University of Bergen, NorwayInstituteProviderUiBInstituteProviderBioMercatorBioMercator is a software that provides a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis, graphical representation of large datasets. User may import sequence and genome annotations datasets within the software in order to display functional annotation related to QTL and meta-QTL.https://sourcesup.renater.fr/projects/biomercatorBioMercatorbiotools:BioMercator4.2.3Desktop applicationhttp://edamontology.org/topic_3055Quantitative geneticshttp://edamontology.org/topic_0780Plant biologyLinuxWindowsMacJavaGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_2944Physical mappinghttp://edamontology.org/data_1860QTL maphttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1288Genome maphttp://edamontology.org/format_1975GFF3https://sourcesup.renater.fr/frs/?group_id=2301Binaries4.2.310.1093/bioinformatics/bth230150598203BigSeqKitThe Next Generation Sequencing (NGS) raw data are stored in FASTA and FASTQ text-based file formats. Common operations on FASTA/Q files include searching, filtering, sampling, deduplication and sorting, among others. We can find several tools in the literature for FASTA/Q file manipulation but none of them are well fitted for large files of tens of GB (likely TBs in the near future) since mostly they are based on sequential processing. The exception is seqkit that allows some routines to use a few threads but, in any case, the scalability is very limited. To deal with this issue, we introduce BigSeqKit, a parallel toolkit to manipulate FASTA/Q files at scale with speed and scalability at its core. BigSeqKit takes advantage of an HPC-Big Data framework (IgnisHPC) to parallelize and optimize the commands included in seqkit. In this way, in most cases it is from tens to hundreds of times faster than other state-of-the-art tools such as seqkit, samtools and pyfastx.https://github.com/citiususc/BigSeqKitbigseqkitbiotools:bigseqkitLibraryCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxPythonGPL-3.0http://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_0372DNA transcriptionhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAPLASTPLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a "seed-and-extend approach" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes.https://github.com/tischulz1/plastpangenome-blastbiotools:pangenome-blast0.0.1-0.2.0Command-line toolhttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0080Sequence analysisLinuxMacWindowsC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1211unambiguous pure nucleotidehttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_3975GFA 1http://edamontology.org/format_2333Binary formatIn order to search for alignments within the pangenome graph,
A pangenome graph used to search for alignments consists of (1) a file in GFA format containing all sequences of the graph, (2) a binary file produced by the tool itself or the software "Bifrost" and (3) a program-specific index data structure in binary format.PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLinehttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1930FASTQIf a pangenome graph already exists and only an index has to be built, FASTA/FASTQ files are not needed.PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fastahttps://gitlab.ub.uni-bielefeld.de/gi/plastRepositoryhttps://github.com/tischulz1/plastMirrorhttps://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.mdGeneral10.1093/bioinformatics/btab07733532821PMC8388040PrimaryMethodBenchmarking studyBielefeld Universityhttps://www.uni-bielefeld.de/InstituteProviderGenome Informaticshttps://gi.cebitec.uni-bielefeld.de/InstituteProviderTizian Schulzplast-service@cebitec.uni-bielefeld.dehttps://orcid.org/0000-0003-0744-7078PersonDeveloperESIprotCharge state determination and molecular weight calculation for low resolution electrospray ionization data.https://nube-gran.de/esiprotesiprotbiotools:esiprotWeb applicationDesktop applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacPythonGPL-3.0ms-utilsProteomicshttp://edamontology.org/operation_0398Protein molecular weight calculationhttp://edamontology.org/operation_2929Protein fragment weight comparisonhttp://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3245Mass spectrometry data formathttp://www.bioprocess.org/esiprot/esiprot_form.phpMirrorhttp://ms-utils.orgSoftware cataloguehttp://www.bioprocess.org/esiprot/esiprot.zipSource codehttp://www.bioprocess.org/esiprot/esiprot.zipSource codehttp://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprotGeneral10.1002/rcm.438420049890Robert Winklerrobert.winkler@ira.cinvestav.mxPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorkollaRkollaR is an open-source R library for eye-tracking analysis and visualization, offering functions for event detection, AOI-based analyses, and algorithm comparison. It provides implementations of several algorithms and includes visualizations for data exploration.https://CRAN.R-project.org/package=kollaRkollarbiotools:kollarhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_2815Human biologyRGPL-3.0http://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_0337Visualisation10.3758/S13428-025-02903-Z41361102PMC12685970Johan Lundin Klebergjohan.lundin.kleberg@su.sePersonProAEProAE is an R package and collection of SAS macros designed for standardized analysis and graphical representation of patient-reported outcomes and adverse events data, specifically focusing on PRO-CTCAE.https://duecklab.github.io/proae.htmlproaebiotools:proaehttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3068Literature and languageRGPL-3.0http://edamontology.org/operation_3435Standardisation and normalisationhttps://CRAN.R-project.org/package=ProAERepository10.1186/S12911-025-03320-041422214Amylou C Dueckdueck.amylou@mayo.eduPersonPv3RsPv3Rs is an R package that allows users to infer the cause (recrudescence, relapse, or reinfection) of Plasmodium vivax malaria recurrence using genetic data. It implements a statistical model to compute posterior probabilities of recurrence states and is freely available on CRAN under the GNU license.https://cran.r-project.org/web/packages/Pv3Rs/index.htmlpv3rsbiotools:pv3rshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3305Public health and epidemiologyRGPL-3.0http://edamontology.org/operation_3664Statistical modellinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/operation_0337Visualisation10.1093/BIOINFORMATICS/BTAF64341324557PMC12758599Aimee R Tayloraimee.taylor@pasteur.frPersonPSQANPSQAN is a Snakemake and R workflow designed to prioritize high-confidence and biologically relevant transcripts from long-read RNA sequencing data, facilitating the interpretation of transcript characterization results.https://github.com/sid-sethi/PSQANpsqanbiotools:psqanhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_4056Long-read sequencinghttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0769WorkflowsRGPL-3.0http://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_0337Visualisation10.1093/BIOADV/VBAF29341394080PMC12701792Siddharth Sethisiddharth.sethi@astx.comhttps://orcid.org/0000-0002-4398-4295PersonMina Rytenmr2022@medschl.cam.ac.ukhttps://orcid.org/0000-0001-9520-6957PersonRISKRISK is a tool for biological network annotation and visualization that integrates community detection algorithms and overrepresentation analysis. It supports diverse network types and generates publication-ready visualizations, demonstrating scalability and adaptability for modern network analysis.https://github.com/riskportal/riskriskbiotools:riskhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3318Physicshttp://edamontology.org/topic_2269Statistics and probabilityPythonGPL-3.0http://edamontology.org/operation_0276Protein interaction network analysishttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_3501Enrichment analysis10.1093/BIOINFORMATICS/BTAF66941423796PMC12766918Hannes Rösthannes.rost@utoronto.cahttps://orcid.org/0000-0003-0990-7488PersonWatConWatCon is a Python package for analyzing conserved water networks across protein families using both dynamic and static structural information. It enables classification of water network conservation, characterization of water networks, and projection of results for visual interpretation.https://watcon.readthedocs.iowatconbiotools:watconhttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0593NMRhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0154Small moleculesPythonGPL-3.0http://edamontology.org/operation_0387Molecular surface calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0321Protein structure validation10.1021/JACSAU.5C0044741450622PMC12728608Shina C. L. Kamerlinskamerlin3@gatech.eduhttps://orcid.org/0000-0002-3190-1173Person