CDS-DBDatabase for patient-derived gene expression signatures induced by cancer treatment.http://cdsdb.ncpsb.org.cn/cds-dbbiotools:cds-dbDatabase portalhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0622GenomicsMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_3463Expression correlation analysis10.1093/NAR/GKAD88837889038PMC10767794Zhongyang Liuliuzy1984@163.comhttps://orcid.org/0000-0002-3371-2392PersonFuchu Hehefc@nic.bmi.ac.cnPersonDong Lilidong.bprc@foxmail.comhttps://orcid.org/0000-0002-8680-0468PersonFLAREFLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that builds on the outputs of the SAILOR edit site discovery tool to identify regions statistically enriched for RNA editing. FLARE can be configured to analyze any type of RNA editing, including C to U and A to I.https://github.com/YeoLab/FLAREflare_rnabiotools:flare_rnaWorkflowhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3794RNA immunoprecipitationPythonFree of chargeOpen accesshttp://edamontology.org/operation_3096Editinghttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_3902RNA binding site prediction10.1186/S12859-023-05452-437784060PMC10544219Gene W. Yeogeneyeo@ucsd.eduhttps://orcid.org/0000-0002-0799-6037PersonEric KofmanPersonOPUS-Fold3Gradient-based protein all-atom folding and docking framework on TensorFlow.http://github.com/OPUS-MaLab/opus_fold3opus-fold3biotools:opus-fold3Workflowhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0203Gene expressionPythonFree of chargeOpen accesshttp://edamontology.org/operation_3899Protein-protein dockinghttp://edamontology.org/operation_0480Side chain modellinghttp://edamontology.org/operation_0479Backbone modelling10.1093/BIB/BBAD36537833840Gang XuPersonJianpeng Majpma@fudan.edu.cnPersonKSFinderKnowledge graph model for link prediction of novel phosphorylated substrates of kinases. KSFinder changes based on major revision comments from PeerJ.https://github.com/manju-anandakrishnan/ksfinder/ksfinderbiotools:ksfinderCommand-line toolhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0218Natural language processinghttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksMacLinuxWindowsPythonFree of chargeOpen accesshttp://edamontology.org/operation_0417PTM site predictionhttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_2489Subcellular localisation prediction10.7717/PEERJ.1616437818330PMC10561642Manju Anandakrishnanmanjua@udel.eduPersonCathy H. WuPersoniDRPro-SCIdentifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers.http://bliulab.net/iDRPro-SCidrpro-scbiotools:idrpro-scWeb applicationhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3125DNA binding siteshttp://edamontology.org/topic_0634PathologyMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_3901RNA-binding protein predictionhttp://edamontology.org/operation_3900DNA-binding protein predictionhttp://edamontology.org/operation_0420Nucleic acids-binding site prediction10.1093/BIB/BBAD25137405873Ke Yankyan@bliulab.netPersonHao Wuhwu@bliulab.netPersonBacSeqAutomated pipeline for whole-genome sequence analysis of bacterial genomes.https://github.com/mecobpsu/bacseqbacseqbiotools:bacseqWorkflowhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3301MicrobiologyJavaShellFree of chargeOpen accesshttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_3840Multilocus sequence typinghttp://edamontology.org/operation_0324Phylogenetic analysis10.3390/MICROORGANISMS1107176937512941PMC10385524Kamonnut Singkhamananskamonnu@medicine.psu.ac.thhttps://orcid.org/0000-0002-0063-7787PersonKomwit Surachatkomwit.s@psu.ac.thhttps://orcid.org/0000-0001-7793-7561PersonAGHmatrixAGHmatrix software is an R-package to build relationship matrices using pedigree (A matrix) and/or molecular markers (G matrix) with the possibility to build a combined matrix of Pedigree corrected by Molecular (H matrix). The package works with diploid and autopolyploid data.https://cran.r-project.org/web/packages/AGHmatrix/index.htmlaghmatrixbiotools:aghmatrixLibraryhttp://edamontology.org/topic_3974Epistasishttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3517GWAS studyRGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3891Essential dynamicshttps://github.com/rramadeu/AGHmatrixRepository10.1093/BIOINFORMATICS/BTAD44537471595PMC10371492Luís Felipe V Ferrãolferrao@ufl.eduhttps://orcid.org/0000-0002-9655-4838PersonRodrigo R AmadeuPersonFASTdRNAFastdRNA: a workflow for analysis of ONT direct RNA seq dataset.https://github.com/Tomcxf/FASTdRNAfastdrnabiotools:fastdrnaWorkflowhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0203Gene expressionPythonRMITFree of chargeOpen accesshttp://edamontology.org/operation_3185Base-callinghttp://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_0428PolyA signal detectionhttp://edamontology.org/operation_3431Deposition10.1093/BIOADV/VBAD09937521311PMC10375421Bosheng Libosheng.li@pku-iaas.edu.cnhttps://orcid.org/0000-0002-1816-7007PersonXiaofeng ChenPersonLZerDWeb server for protein-protein docking prediction using the LZerD algorithm.https://lzerd.kiharalab.orglzerd_webbiotools:lzerd_webWeb applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysisFree of chargeOpen accesshttp://edamontology.org/operation_3899Protein-protein dockinghttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/operation_0570Structure visualisation10.1007/978-1-0716-3327-4_2837450159PMC10561630Daisuke Kiharadkihara@purdue.eduPersonKannan HariniPersonICAnnoLncRNASnakemake Pipeline for a long non-coding-RNA search and annotation in transcriptomic sequences.https://github.com/artempronozin95/ICAnnoLncRNA-identification-classification-and-annotation-of-LncRNAicannolncrnabiotools:icannolncrnaWorkflowhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3512Gene transcriptsPythonRFree of chargeOpen accesshttp://edamontology.org/operation_3258Transcriptome assemblyhttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3695Filteringhttp://edamontology.org/operation_0524De-novo assembly10.3390/GENES1407133137510236PMC10379598Artem Yu. Pronozinpronozinartem95@gmail.comhttps://orcid.org/0000-0002-3011-6288PersonDmitry A AfonnikovPerson