Purna AIAI Agent for Biomedical Researchhttps://purna.aipurna_aibiotools:purna_aiProprietaryEmergingFree of charge (with restrictions)Open access (with restrictions)AgentomicsAutonomous ML experimentation for biomedical data.https://www.agentomicsml.com/agentomicsbiotools:agentomicsMITFree of chargeOpen accesshttps://www.agentomicsml.com/Otherhttps://github.com/BioGeMT/agentomics-mlRepositoryhttps://biogemt.github.io/agentomics-ml/User manual10.1093/bioinformatics/btag25042412783sciagentkitSciAgentKit is an MCP-native toolkit that connects AI agents to reproducible computational drug-discovery workflows. It integrates established tools for molecular analysis, protein-structure assessment, binding-site detection, molecular docking, molecular dynamics, trajectory analysis and scientific reporting.https://sciagentkit.com/sciagentkitbiotools:sciagentkitVersion 1.0.3Command-line toolBioinformatics portalWorkflowhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_2258CheminformaticsMacLinuxPythonProprietaryEmergingCommercialhttps://sciagentkit.comOtherhttps://sciagentkit.com/#installDownloads pageTrace4MedicalImageCleaningTrace4MedicalImageCleaning™ is a tool aimed at automatically detecting and removing text in medical images, with a specific focus on 2D ultrasound and mammography studies.http://deeptracetech.com/trace4medicalimagecleaningbiotools:trace4medicalimagecleaning1.0LibraryLinuxWindowsMATLABPythonProprietaryEUCAIMEmergingCommercialRestricted accesshttps://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/trace4medicalimagecleaning/artifacts-tabRepositoryHarbor linkNIM-StudioNIM Studio is a local-first platform for neuroinformatics, BIDS organization, metadata generation, duplicate auditing, and scalable research data management.https://nim-studio.readthedocs.io/en/latest/index.htmlnim-studiobiotools:nim-studio0.1.0-betaDesktop applicationhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_4010Open scienceWindowsMacPythonProprietaryEmergingFree of chargeOpen access (with restrictions)http://edamontology.org/operation_2409Data handling10.5281/zenodo.21296290.0.1.0-betaGAIn (Genomic Annotation Infrastructure)GAIn is a platform for annotating genetic variants, genomic positions, and regions with reproducible, declarative pipelines using curated Genomic Resource Repositories.https://gain.iossifovlab.com/gain_genomic_annotation_infrastructurebiotools:gain_genomic_annotation_infrastructureWeb applicationCommand-line toolhttp://edamontology.org/topic_0622GenomicsLinuxMacPythonMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_1016Sequence positionhttp://edamontology.org/data_1276Nucleic acid featureshttp://edamontology.org/data_1017Sequence range

http://edamontology.org/data_1276Nucleic acid features

Annotates tabular files containing genetic variants, genomic positions, or genomic regions using a declarative YAML pipeline and configured Genomic Resource Repositories.annotate_tabular variants.tsv pipeline.yaml -o annotated_variants.tsvhttps://github.com/iossifovlab/gainRepositoryhttps://github.com/iossifovlab/mini-GRRRepositoryhttps://github.com/iossifovlab/gain/archive/refs/heads/master.zipSource codehttps://iossifovlab.com/gaindocs/General10.64898/2026.07.08.737273PreprintMurat Cokolmuratcokol@gmail.comApis-wings-NW-EuropeThe dataset consists of 29,043 images of the fore wing of the honey bee (Apis mellifera) worker and represents 1,342 samples from ten countries in northwestern Europe.https://zenodo.org/records/18845767apis-wings-nw-europebiotools:apis-wings-nw-europehttps://zenodo.org/records/18845767RepositoryTranscriptoScopeLocal Windows-friendly R Shiny application for RNA-seq differential expression using DESeq2, normalized-expression testing, over-representation analysis, fgsea-ranked pathway analysis, and WGCNA coexpression-network analysis. It supports input validation, additive and interaction designs, built-in human, fruit-fly, and yeast annotations, publication-quality plots, and reproducibility bundles containing results, settings, and executable R and R Markdown rerun code.https://github.com/Shettima123/TranscriptoScopetranscriptoscopebiotools:transcriptoscope0.4.9Desktop applicationWorkbenchhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3170RNA-SeqWindowsRMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_3680RNA-Seq analysishttp://edamontology.org/operation_3766Weighted correlation network analysishttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_3928Pathway analysishttps://github.com/Shettima123/TranscriptoScopeRepositoryhttps://github.com/Shettima123/TranscriptoScope/issuesIssue trackerhttps://github.com/Shettima123/TranscriptoScope/releases/download/v0.4.9/TranscriptoScope_Windows_Store_v0.4.9.exeBinariesStandalone x64 Windows installer that bundles R and the required package library.0.4.9https://github.com/Shettima123/TranscriptoScope/releases/download/v0.4.9/TranscriptoScope_Windows_v0.4.9.zipSoftware packageManual Windows package for users who already have R.0.4.9https://github.com/Shettima123/TranscriptoScope/archive/refs/tags/v0.4.9.zipSource code0.4.9https://github.com/Shettima123/TranscriptoScope/releases/tag/v0.4.9Downloads page0.4.9https://github.com/Shettima123/TranscriptoScope/blob/v0.4.9/README.mdGeneralhttps://github.com/Shettima123/TranscriptoScope/blob/v0.4.9/INSTALL_WINDOWS.mdInstallation instructionsQuick start guidehttps://github.com/Shettima123/TranscriptoScope/blob/v0.4.9/RELEASE_NOTES.mdRelease noteshttps://github.com/Shettima123/TranscriptoScope/blob/v0.4.9/CITATION.cffCitation instructionshttps://github.com/Shettima123/TranscriptoScope/blob/v0.4.9/SUPPORT.mdGeneralSupport and issue-reporting instructions.10.5281/zenodo.21331626Primary0.4.9Version-specific archived software release.Abubakar Abdulkadirhttps://github.com/Shettima123PersonDeveloperMaintainerDocumentorPrimary contactDr. Rosby's LabProjectProviderSupportSouthern University A and MInstituteProviderVigyanllmVigyanLLM is a sovereign, on-premises biomedical AI platform designed for computational biology. It provides autonomous primer design, evaluating melting temperature (Tm) and GC content; CRISPR guide RNA analysis with off-target scoring; BLAST sequence similarity searching; multiple sequence alignment (MSA); and GPU-accelerated molecular docking for drug discovery. Unlike cloud-based SaaS, VigyanLLM deploys via Docker to ensure institutional genomic data sovereigntyhttps://www.vigyanllm.in/vigyanllmbiotools:vigyanllmBioinformatics portalhttp://edamontology.org/topic_4019BiosciencesProprietaryEmergingFree of charge (with restrictions)Open accessFolkloreDeterministic, rule-based variant interpretation platform for clinical genetics laboratories. Automates ACMG/AMP 2015 classification using a Bayesian point-based framework (Tavtigian et al. 2018) with BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022). Integrates 8 reference databases (gnomAD v4.1, ClinVar, dbNSFP 4.9c, SpliceAI, gnomAD Constraint, HPO, ClinGen, Ensembl VEP). Analyzes nuclear and mtDNA variants, structural and copy-number variants (SV/CNV), with trio/family and cohort analysis. Supports HPO-based phenotype matching, biomedical literature mining across 2M+ PubMed publications, and structured clinical report generation. AI assists in evidence synthesis but does not make classification decisions. EU-hosted on dedicated infrastructure in Helsinki, Finland (GDPR-compliant).https://folklore.helena.bioHelixInsightbiotools:HelixInsight3.39.1RRID:SCR_028669rrid3.39.1Web applicationhttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3063Medical informaticsLinuxPythonProprietaryEmergingCommercialRestricted accesshttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCF

http://edamontology.org/data_2955Sequence report

http://edamontology.org/data_0920Genotype/phenotype report

http://edamontology.org/data_1622Disease report

http://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_0305Literature searchhttp://edamontology.org/operation_0362Genome annotationhttps://folklore.helena.bio/docsGeneralComplete production documentation covering every threshold, database version, and classification rule. Intended for clinical geneticists, laboratory directors, accreditation auditors, and bioinformaticians.https://folklore.helena.bio/how-it-worksGeneralSeven-stage analysis pipeline (quality control, annotation, classification, phenotype matching, literature, screening, interpretation) transforming a raw VCF into a clinician-ready report, each stage producing traceable, auditable output.https://folklore.helena.bio/methodologyGeneralACMG/AMP 2015 classification methodology (Richards et al. 2015) via Bayesian point-based system (Tavtigian et al. 2018), BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022), and SpliceAI aligned to ClinGen SVI 2023 (Walker et al. 2023). Optional ClinGen VCEP overlay for ~50-60 genes. Strictly evidence-based, no ML determines pathogenicity.https://folklore.helena.bio/methodology/mtdnaGeneralMitochondrial DNA variant classification under the ClinGen Mitochondrial Disease Working Group (MMDWG) 2020 specification (McCormick et al. 2020). Operates as an independent module from the nuclear ACMG/AMP pipeline; every variant carries an explicit framework provenance label. Strength tiers follow ClinGen mtDNA VCEP v1.0.0.https://folklore.helena.bio/methodology/family-analysisGeneralInheritance-aware evidence from trio (proband + both parents), duo, and proband-plus-sibling analyses. Implements ClinGen SVI 2018 de novo PS2/PM6 (PMID 29543229), Jarvik & Browning 2016 LOD segregation framework (PMID 27236918), and ClinGen SVI 2021 PP1 strength bands. Augments the existing ACMG/AMP classification without re-calling variants.https://folklore.helena.bio/methodology/svGeneralStructural and copy-number variant evaluation under the Riggs 2020 joint ACMG/ClinGen technical standard. Documents the point-based loss and gain metrics, dosage-sensitivity evidence, and five-tier classification, with reference data and documented limitations.https://folklore.helena.bio/screening-methodologyGeneralPrioritizes classified variants for clinical review. After ACMG classification determines what each variant is, screening determines which to review first based on patient-specific clinical relevance. Evaluates seven independent dimensions, applies clinical profile boosts, and produces a four-tier priority ranking with transparent, visible score components.10.5281/zenodo.21105027Preprint1.0Methodological framework for real-world performance studies of the platform's variant classification, demonstrated on three internal validation cohorts.10.5281/zenodo.21189571Preprint1.0A Deterministic Classification Core with an Agentic Interpretation Layer: An Architecture for Auditable, Human-Gated Clinical Variant AnalysisHelena Bioinformaticscontact@helena.biohttps://helena.bioInstituteDeveloperpickletFree, browser-based tool to open almost any sequence file — FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, AB1/ABIF, Clustal, Stockholm, PHYLIP, NEXUS, MSF, PIR and more — see every sequence inside, pick the ones you want, and save them as FASTA. Runs entirely in your browser — your data never leaves your machine.https://fishka.bio/pickletpickletbiotools:pickletWeb applicationDesktop applicationhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0077Nucleic acidsFreewareMatureab1lensBrowser-based tool for viewing, comparing, and inspecting Sanger sequencing ab1 / ABIF chromatogram files. Files are processed locally in the browser.https://fishka.bio/ab1lensab1lensbiotools:ab1lensWeb applicationDesktop applicationhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3673Whole genome sequencingFreewareMatureFree of chargeOpen accesslinkset-automationlinkset-automation is a set of tools to automatically generates CyTargetLinker linksets from different resources, starting with WikiPathways.https://github.com/CyTargetLinker/linkset-automationlinkset-automationbiotools:linkset-automationCommand-line toolhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0092Data visualisationShellPythonApache-2.0EmergingFree of chargehttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/data_2093Data referencehttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2093Data referencehttp://edamontology.org/format_3618xgmml

https://github.com/CyTargetLinker/linkset-automationRepositoryhttps://github.com/CyTargetLinker/linkset-automation/archive/refs/heads/main.zipSource codehttps://github.com/CyTargetLinker/linkset-automation/blob/main/README.mdCommand-line optionswikipathwaysusescytoscapeusesbridgedbuses10.12688/f1000research.14613.231489175PMC6707396Primary10.1186/s13059-019-1758-431477170PMC6717989OtherGeneral description of automation in Cytoscapepico_galaxyShort Python script (using Biopython library functions) to extract sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given by a column of a tabular file. The output order follows that of the tabular file, and if there are duplicates in the tabular file, there will be duplicates in the output sequence file.https://github.com/peterjc/pico_galaxy/seq_select_by_idpico_galaxybiotools:pico_galaxyv0.0.15Command-line toolhttp://edamontology.org/topic_3307Computational biologyShellPythonNot licensedMatureFree of chargehttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_3607qualhttp://edamontology.org/format_3284SFFhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_3284SFFhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

figtracerPlain-text, git-tracked electronic lab notebook (ELN) for reproducible bioinformatics — threads your R & Python figures into living lab notes with full provenance. Built for single-cell / CyTOF / flow cytometry; works with Obsidian, Quarto & Jupyter.https://github.com/david-priest/figtracerfigtracerbiotools:figtracer0.1.0LibraryCommand-line toolhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3934Cytometryhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_3372Software engineeringPythonMITEmergingFree of chargeOpen access10.5281/zenodo.21288980David Priesthttps://orcid.org/0000-0003-0095-6718InstituteKraken2TaxThis tool converts data from Kraken to a Galaxy taxonomy representation.https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2taxkraken2taxbiotools:kraken2taxhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/operation_3434Conversion10.1186/gb-2014-15-3-r4624580807PMC405381310.1101/gr.094508.10919819906PMC2775585mothurOpen-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.01541-0919801464PMC2786419anndataFrom https://anndata.readthedocs.io/en/latest/ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray."https://github.com/scverse/anndataanndatabiotools:anndataCommand-line toolPythonBSD-3-Clausehttps://anndata.readthedocs.io/en/latest/General10.1101/2021.12.16.473007Summarize taxonomyGiven taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks." - Galaxy tool wrapperhttps://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_reportt2t_reportbiotools:t2t_reporthttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/operation_3793Read summarisationhttp://edamontology.org/operation_2990Classificationhttps://github.com/onecodex/taxonomy/Repositoryhttps://docs.rs/taxonomy/latest/taxonomy/json/enum.JsonFormat.htmlUser manualDraw phylogeny"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapperhttps://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2pst2psbiotools:t2pshttp://edamontology.org/topic_0194Phylogenomicshttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttps://github.com/galaxyproject/tools-devteam/blob/9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml#L51GeneralFormat metaphlan2 outputThis tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_outputformat_metaphlan2_outputbiotools:format_metaphlan2_outputhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/operation_0335FormattingCompare HUMAnN2 outputsThis tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several sampleshttps://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_outputcompare_humann2_outputsbiotools:compare_humann2_outputshttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/operation_2424ComparisonCombine Metaphlan and HUMAnNThis tool combine MetaPhlAn outputs and HUMANnN outputshttps://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humanncombine_metaphlan_and_humannbiotools:combine_metaphlan_and_humannhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/operation_3436AggregationFind lowest diagnostic rank"This tool identifies the lowest taxonomic rank for which a metagenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input." - Galaxy tool wrapperhttps://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapperlca1biotools:lca1http://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/operation_3460Taxonomic classificationMultispecies Orthologous MicrosatsThis tool extracts / finds orthologous microsatellite blocks for >2 species alignments.https://github.com/galaxyproject/tools-devteam/tree/4066016ffafd7918ba9826db4f3c6fb41315e942/tools/multispecies_orthologous_microsatsmultispecies_orthologous_microsatsbiotools:multispecies_orthologous_microsatshttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0157Sequence composition, complexity and repeatsLegacyhttp://edamontology.org/operation_3194Genome feature comparisongi2taxonomyThe tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomygi2taxonomybiotools:gi2taxonomyhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3282ID mappingqualityFilterQuality score based filtering of nucleotides.https://github.com/galaxyproject/tools-devteam/tree/4066016ffafd7918ba9826db4f3c6fb41315e942/tools/quality_filterqualityfilterbiotools:qualityfilterhttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_3572Data quality managementhttp://edamontology.org/operation_3218Sequencing quality controlSeqBenchSeqBench is a browser-based toolkit for DNA, RNA and protein sequence analysis: primer design, restriction digest and cloning simulation, CRISPR guide design, codon optimization, pairwise alignment and plasmid annotation. Supports batch FASTA processing and multi-tool workflow pipelines, and every tool is also exposed as a REST API and MCP server for scripted or agent-driven use. All computation runs client-side in the browser, so input sequences are never uploaded to a server.https://seqbench.comseqbench-onlinebiotools:seqbench-onlineWeb applicationhttp://edamontology.org/topic_0080Sequence analysisFreewareEmergingFree of chargehttp://edamontology.org/operation_0431Restriction site recognitionhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_0455Nucleic acid thermodynamic property calculationhttp://edamontology.org/operation_0236Sequence composition calculationhttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/operation_0284Codon usage table generationhttps://seqbench.com/api/mcpServiceMCP (Model Context Protocol) server endpoint exposing all tools for agent-driven / scripted use.https://seqbench.com/api/v1ServiceREST API base URL. Every tool is available as an endpoint (POST /api/v1/tool-name), plus batch and workflow endpoints for scripted/programmatic use.thromboSeqthromboSeq 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 format

http://edamontology.org/data_2955Sequence report

10.3390/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_2968Image

http://edamontology.org/data_2884Plot

10.3389/fonc.2021.62309833777768PMC7988092PrimarycTTNcTTN is a set of R scripts for analyzing genetic constraint in the TTN gene by adjusting for sequencing depth and calculating constraint metrics with confidence intervals. It includes tools for obtaining observed and expected variant counts from gnomAD exome data.https://github.com/ImperialCardioGenetics/cTTNcTTNbiotools:cTTNLibraryhttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_0622GenomicsRNot licensedEmerginghttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2884Plot

ggplot2uses10.1161/circulationaha.120.05045533583186PMC8032209Primaryaustraitsaustraits is an R package for accessing the AusTraits Plant database and working with traits.build databaseshttps://traitecoevo.github.io/austraitsaustraitsbiotools:austraitsv3.1.0Database portalLibraryhttp://edamontology.org/topic_0780Plant biologyRMITMaturehttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2884Plot

https://traitecoevo.github.io/austraitsGeneralhttps://traitecoevo.github.io/austraits/articles/austraits.htmlInstallation instructionsQuick start guide10.1038/s41597-021-01006-6PrimaryFQM_AnalysisFully automatic CAC scoring analysis of QRM CCI inserthttps://github.com/nwerf/FQM_AnalysisFQM_Analysisbiotools:FQM_Analysishttp://edamontology.org/topic_3452TomographyMATLABPythonNot licensedEmerginghttp://edamontology.org/operation_3438Calculationhttp://edamontology.org/data_2968Image

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3620xlsx

10.1002/mp.1491233932026PMC8360117PrimaryCis-mQTL-mapping-protocol-for-methylomeCis-mQTL mapping protocol for placental methylome using TensorQTL, providing a step-by-step guide for genotype QC, imputation, and analysis with detailed scripts and commands.https://github.com/ariadnacilleros/Cis-mQTL-mapping-protocol-for-methylomeCis-mQTL-mapping-protocol-for-methylomebiotools:Cis-mQTL-mapping-protocol-for-methylomev.1.0.0http://edamontology.org/topic_0625Genotype and phenotypeRPerlNot licensedMaturehttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_3288PED/MAP

http://edamontology.org/data_1860QTL maphttp://edamontology.org/format_2333Binary format

https://github.com/ariadnacilleros/Cis-mQTL-mapping-protocol-for-methylome/wikiGeneral10.1038/s41467-025-57760-340087310PMC11909199PrimaryORIONORION is a python package that ingests datasets from diverse knowledge bases and transforms them into modular, interoperable knowledge graphs. It also provides general functionality for manipulating and normalizing KGX files and metadata.https://github.com/RobokopU24/ORION/robokop-orionbiotools:robokop-orionv1.3.3DICHROWEBA server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.http://dichroweb.cryst.bbk.ac.uk/html/home.shtmldichrowebbiotools:dichrowebRRID:SCR_018125rridWeb applicationhttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMachttp://edamontology.org/operation_2488Protein secondary structure comparisonhttp://edamontology.org/operation_0319Protein secondary structure assignmenthttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_2416Protein secondary structure analysishttp://dichroweb.cryst.bbk.ac.uk/html/userguide_dichroweb.shtmlGeneral10.1093/nar/gkh37115215473PMC44150910.1093/bioinformatics/18.1.21111836237Contact Formhttp://dichroweb.cryst.bbk.ac.uk/html/bugreport.shtmlPersonPrimary contactpyBiodatafusePython package for biodatafuse project.https://biodatafuse.org/pyBiodatafusebiotools:pyBiodatafusev1.3.0Database portalhttp://edamontology.org/topic_3344Biomedical sciencePythonC++MITMaturehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/data_1052URL

http://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_3477Cytoscape input file formathttp://edamontology.org/format_3617Graph format

https://biodatafuse.github.io/pyBiodatafuseGeneralhttps://pybiodatafuse.readthedocs.io/en/latest/index.htmlInstallation instructionsUser manual10.1093/bioinformatics/btag06441692987PMC12949461PrimaryAmsterdamUMCdbAmsterdamUMCdb is a database of de-identified health data related to tens of thousands of intensive care unit admissions, including demographics, vital signs, laboratory tests and medications.https://amsterdammedicaldatascience.nl/AmsterdamUMCdbbiotools:AmsterdamUMCdb1.5.0Database portalhttp://edamontology.org/topic_3303MedicinePythonMITMaturehttp://edamontology.org/operation_0224Query and retrievalhttps://github.com/AmsterdamUMC/AmsterdamUMCdb/wikiGeneral10.1097/ccm.000000000000491633625129PMC8132908PrimaryRAiSD-AIRAiSD-AI is a tool for training, testing, and deploying Convolutional Neural Networks to detect selective sweeps in genomic data, extending the functionality of the original RAiSD software with machine learning capabilities. It supports SNP data processing, CNN model training with TensorFlow or PyTorch, and genome-wide selective sweep detection.https://github.com/alachins/RAiSD-AIRAiSD-AIbiotools:RAiSD-AI4.5Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3474Machine learningShellRPythonCNot licensedMatureFree of chargehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2048Report

10.1038/s42003-018-0085-830271960PMC6123745Method10.32942/x2gw9bPrimaryValidSenseValidSense is a toolbox for assessing agreement between two quantitative methods or devices measuring the same quantity using the Limits of Agreement (LoA) analysis, also known as the Bland-Altman analysis.https://github.com/umcu/ValidSenseValidSensebiotools:ValidSensePythonMITEmerginghttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/data_3108Experimental measurementhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3603PNG

10.1016/s0140-6736(86)90837-82868172Method10.1177/09622802990080020410501650Method10.1080/1054340070132942217613642MethodtrieA generic C++ trie search tree library for small alphabets, allowing customizable leaf node structures and supporting approximate matching and word generation.https://github.com/jfjlaros/trietriebiotools:trieLibraryC++MITEmergingFree of chargehttp://edamontology.org/operation_0224Query and retrievalhttps://cpptrie.readthedocs.io/en/latest/User manualInstallation instructionsAPI documentationtosccatoscca is an R package to perform Thresholded Ordered Sparse Canonical Correlation Analysis (TOSCCA).https://github.com/nuria-sv/tosccatosccabiotools:toscca1.0Libraryhttp://edamontology.org/topic_2269Statistics and probabilityROtherEmergingFree of chargehttp://edamontology.org/operation_3935Dimensionality reductionhttp://edamontology.org/operation_3465Correlationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_3869Simulation

http://edamontology.org/data_1636Heat map

http://edamontology.org/data_2884Plot

https://github.com/nuria-sv/toscca/wikiGeneralggplot2uses10.1093/bioadv/vbae02138456127PMC10919946PrimaryminibwaMinibwa aligns short reads against a reference genome. It is the successor of bwa-mem with a different algorithm. Minibwa is over three times as fast as the original bwa-mem and twice as fast as bwa-mem2 at comparable accuracy. While minibwa works with accurate long reads, minimap2 is more robust under high error rate.https://github.com/lh3/minibwaminibwabiotools:minibwaGONetA Molecular Interaction-Guided Graph Learning Framework for Multi-Omics Cancer Classificationhttps://github.com/EayonYang/GONetGONet-v1biotools:GONet-v1http://edamontology.org/topic_4021Multiomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3474Machine learningPythonApache-2.0OpenProteoOpenProteo is the open-source Rust stack for proteomics raw-file access. It reads Thermo, Bruker, and Waters acquisitions through a single API (via the sibling OpenTFRaw, OpenTimsTDF, and OpenWRaw readers), converts them to PSI-MS mzML 1.1.0 with a canonical writer, and provides a zero-copy read_arrow() API (enabled by default) that loads directly into Polars or Pandas via PyArrow. No vendor SDKs, no Windows-only DLLs, no binary blobs in the release pipeline. Includes a one-shot vendor2mzml CLI.https://github.com/Sigilweaver/OpenProteoOpenProteobiotools:OpenProteo1.0.3doi:10.5281/zenodo.20470595doiCommand-line toolLibraryhttp://edamontology.org/topic_0121ProteomicsWindowsMacLinuxPythonRustApache-2.0EmergingFree of chargehttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_2536Mass spectrometry data

http://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3244mzML

https://github.com/Sigilweaver/OpenProteoRepositoryhttps://crates.io/crates/openproteo-ioSoftware packageRust cratehttps://pypi.org/project/openproteo/Software packagePython packagehttps://github.com/Sigilweaver/OpenProteo/releasesBinariesPre-built vendor2mzml CLI binarieshttps://sigilweaver.app/openproteo/docsUser manualNathan Rileyhttps://orcid.org/0009-0004-1579-7312PersonDeveloperMaintainerOpenWRawOpenWRaw is a standalone, cross-platform reader for Waters MassLynx .raw acquisition directories, implemented in pure Rust with no dependency on vendor DLLs. Python bindings built on PyO3 expose functions, scans, and ion-mobility data as native Python objects from Waters QTof and SYNAPT instrument families, ready to be assembled into a Pandas or Polars DataFrame.https://github.com/Sigilweaver/OpenWRawOpenWRawbiotools:OpenWRaw1.0.5doi:10.5281/zenodo.20470607doiLibraryhttp://edamontology.org/topic_0121ProteomicsWindowsMacLinuxPythonRustApache-2.0EmergingFree of chargehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_2536Mass spectrometry data

http://edamontology.org/data_2536Mass spectrometry data

https://github.com/Sigilweaver/OpenWRawRepositoryhttps://crates.io/crates/openwrawSoftware packageRust cratehttps://pypi.org/project/openwraw/Software packagePython packagehttps://sigilweaver.app/openwraw/docsUser manualNathan Rileyhttps://orcid.org/0009-0004-1579-7312PersonDeveloperMaintainerOpenTimsTDFOpenTimsTDF is a standalone, cross-platform reader for Bruker timsTOF .tdf and .tdf_bin acquisition files, implemented in pure Rust with no dependency on vendor SDKs. Python bindings built on PyO3 expose frame, scan, and peak data as native Python objects, providing ion-mobility-aware access that can be assembled into a Pandas or Polars DataFrame.https://github.com/Sigilweaver/OpenTimsTDFOpenTimsTDFbiotools:OpenTimsTDF1.0.6doi:10.5281/zenodo.20470603doiLibraryhttp://edamontology.org/topic_0121ProteomicsWindowsMacLinuxPythonRustApache-2.0EmergingFree of chargehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_2536Mass spectrometry data

http://edamontology.org/data_2536Mass spectrometry data

https://github.com/Sigilweaver/OpenTimsTDFRepositoryhttps://crates.io/crates/opentimstdfSoftware packageRust cratehttps://pypi.org/project/opentimstdf/Software packagePython packagehttps://sigilweaver.app/opentimstdf/docsUser manualNathan Rileyhttps://orcid.org/0009-0004-1579-7312PersonDeveloperMaintainerOpenTFRawOpenTFRaw is a standalone, cross-platform reader for Thermo Fisher Scientific .raw mass-spectrometry files, implemented in pure Rust with no dependency on vendor DLLs or .NET. Python bindings built on PyO3 return NumPy arrays for spectral data, straightforward to load into Pandas or Polars. Covers format versions 8 through 66 (LCQ Classic through Orbitrap Astral and modern TSQ instruments), supporting both centroid and profile spectra.https://github.com/Sigilweaver/OpenTFRawOpenTFRawbiotools:OpenTFRaw1.0.6doi:10.5281/zenodo.20470601doiLibraryhttp://edamontology.org/topic_0121ProteomicsWindowsLinuxMacPythonRustApache-2.0EmergingFree of chargehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_2536Mass spectrometry data

http://edamontology.org/data_2536Mass spectrometry data

https://github.com/Sigilweaver/OpenTFRawRepositoryhttps://crates.io/crates/opentfrawSoftware packageRust cratehttps://pypi.org/project/opentfraw/Software packagePython packagehttps://sigilweaver.app/opentfraw/docsUser manualNathan Rileyhttps://orcid.org/0009-0004-1579-7312PersonDeveloperMaintainerHPO ExplorerInteractive browser for the complete Human Phenotype Ontology (~19,800 terms), with a graph-based term explorer and a clinical profile analyzer for phenotype similarity, differential diagnosis, and gene prioritization.https://hpoexplorer.comhpo_explorerbiotools:hpo_explorer0.1.0Web applicationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3325Rare diseasesJavaScriptTypeScriptCC-BY-4.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/data_3025Ontology concept identifier

http://edamontology.org/data_2353Ontology data

Browses the full HPO term graph via a synced tree and Cytoscape DAG view.http://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_1081Genotype and phenotype annotation ID

http://edamontology.org/data_0920Genotype/phenotype report

https://hpoexplorer.com/aboutOtherhttps://hpoexplorer.com/abouthttps://hpoexplorer.com/articlesSoftware cataloguehttps://github.com/mchandrahasreddy/hpoexplorerRepositoryhttps://hpoexplorer.com/articlesGeneralguides and documentation.10.5281/zenodo.21178435Chandrahas Mallireddycontact@hpoexplorer.comhttps://hpoexplorer.comPersonDeveloperChandrahas Mallireddycontact@hpoexplorer.comhttps://hpoexplorer.comPersonPrimary contactBioCalculatorBioCalculator is a mobile toolkit for biology and laboratory calculations. It consolidates calculators and preparation guides for molecular biology, microbiology, virology, stock solutions, buffers, dilutions, unit conversions, and TCID50 endpoint dilution workflows for students and lab professionals.https://biocalculator.app/biocalculatorbiotools:biocalculatorMobile applicationiOSAndroidFreewareMatureFree of chargeOpen accesshttps://apps.apple.com/app/apple-store/id6498629520?pt=126896711&ct=website&mt=8Downloads pageiOS App Store listing for BioCalculator.https://play.google.com/store/apps/details?id=com.biocalculator.appDownloads pageGoogle Play listing for BioCalculator.