SAMSelf-adapting mixture prior to dynamically borrow information from historical data in clinical trials.https://cran.r-project.org/web/packages/SAMpriorsam_clinicalbiotools:sam_clinicalLibraryhttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3325Rare diseasesC++CPythonRBSD-3-Clausehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0335Formattinghttp://edamontology.org/operation_3436Aggregationhttp://project.org/package=SAMpriorOtherhttps://github.com/pengyang0411/SAMpriorRepository10.1111/BIOM.139273772151310.1093/BIB/BBAD32037668049Xiangxiang ZengZengzxeng@hnu.edu.cnPersonDeepCCIA deep learning framework for identifying cell-cell interactions from single-cell rna sequencing data.https://github.com/JiangBioLab/DeepCCIdeepccibiotools:deepcciCommand-line toolhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3474Machine learningMacLinuxWindowsPythonMITFree of chargehttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_0313Expression profile clusteringhttp://edamontology.org/operation_3435Standardisation and normalisation10.1093/BIOINFORMATICS/BTAD59637740953PMC10558043Qinghua Jiangqhjiang@hit.edu.cnhttps://orcid.org/0000-0002-6130-8610PersonZhigang LiuPersonZhaochun Xujdzxuzhaochun@163.comhttps://orcid.org/0000-0003-1799-5529PersonTcbfA novel user-friendly tool for pan-3 d genome analysis of topologically associating domain in eukaryotic organisms.https://github.com/TcbfGroup/Tcbftcbfbiotools:tcbfWorkflowhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_3175Structural variationhttp://edamontology.org/topic_0780Plant biologyLinuxPythonRMITFree of chargehttp://edamontology.org/operation_3182Genome alignment10.1093/BIOINFORMATICS/BTAD57637725346PMC10539074Maojun Wangmjwang@mail.hzau.edu.cnhttps://orcid.org/0000-0002-4791-3742PersonFunTaxIS-liteA simple and light solution to investigate protein functions in all living organisms.https://www.medcomp.medicina.unipd.it/funtaxis-litefuntaxis_litebiotools:funtaxis_liteWeb applicationCommand-line toolhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0621Model organismsMacLinuxWindowsPythonShellFree of chargehttp://edamontology.org/operation_3695Filteringhttp://edamontology.org/operation_2421Database searchhttps://github.com/MedCompUnipd/FunTaxIS-liteRepository10.1093/BIOINFORMATICS/BTAD54937672040PMC10500080Stefano Toppostefano.toppo@unipd.ithttps://orcid.org/0000-0002-0246-3119PersonBiocMAPBioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data.http://research.libd.org/BiocMAP/biocmapbiotools:biocmapWorkflowhttp://edamontology.org/topic_3674Methylated DNA immunoprecipitationhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3419PsychiatryLinuxRPythonFree of chargehttp://edamontology.org/operation_3186Bisulfite mappinghttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_3919Methylation callinghttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3809DMR identificationhttps://github.com/LieberInstitute/BiocMAPRepository10.1186/S12859-023-05461-337704947PMC10498615Leonardo Collado-Torreslcolladotor@gmail.comhttps://orcid.org/0000-0003-2140-308XPersonpLM-BLASTDistant homology detection based on direct comparison of sequence representations from protein language models.https://toolkit.tuebingen.mpg.de/tools/plmblastplm_blastbiotools:plm_blastWeb applicationCommand-line toolhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3299Evolutionary biologyMacLinuxWindowsPythonMITFree of chargehttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2996Structure classificationhttp://edamontology.org/operation_0294Structure-based sequence alignmenthttp://edamontology.org/operation_0496Global alignmenthttps://github.com/labstructbioinf/pLM-BLASTRepository10.1093/BIOINFORMATICS/BTAD57937725369PMC10576641Stanislaw Dunin-Horkawiczstanislaw.dunin-horkawicz@tuebingen.mpg.dehttps://orcid.org/0000-0002-4581-1558PersonePlatypusAn ecosystem for computational analysis of immunogenomics data.http://github.com/alexyermanos/Platypuseplatypusbiotools:eplatypusSuitehttp://edamontology.org/topic_3948Immunoinformaticshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0610EcologyMacWindowsRGPL-3.0Free of chargehttps://cloud.r-project.org/web/packages/Platypus/index.htmlRepository10.1093/BIOINFORMATICS/BTAD55337682115PMC10518073Alexander Yermanosayermanos@gmail.comhttps://orcid.org/0000-0001-6238-0588PersonMuDCoDMulti-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.https://github.com/bo1929/MuDCoDmudcodbiotools:mudcodLibraryhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0602Molecular interactions, pathways and networksMacLinuxWindowsPythonMITFree of chargehttp://edamontology.org/operation_3463Expression correlation analysishttp://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_3927Network analysis10.1093/BIOINFORMATICS/BTAD59237740957PMC10564618Oznur Tastanotastan@sabanciuniv.eduhttps://orcid.org/0000-0001-7058-5372PersonSündüz Keleşkeles@stat.wisc.eduPersonMAVENCompound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny.https://laylagerami.github.io/MAVENmavenbiotools:mavenWeb applicationhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_0749Transcription factors and regulatory sitesLinuxMacRGPL-3.0Free of chargehttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3928Pathway analysishttp://edamontology.org/operation_2489Subcellular localisation predictionhttps://github.com/laylagerami/MAVENRepository10.1186/S12859-023-05416-837715141PMC10502988Layla Hosseini-Geramilaylagerami@hotmail.comhttps://orcid.org/0000-0003-0948-2387PersonAndreas Benderab454@cam.ac.ukPersonFLIBaseA comprehensive repository of full-length isoforms across human cancers and tissues.http://www.FLIBase.orgflibasebiotools:flibaseDatabase portalhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3930ImmunogeneticsMacLinuxWindowsPythonCC-BY-4.0Free of chargehttp://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_3800RNA-Seq quantificationhttp://edamontology.org/operation_0446Exonic splicing enhancer predictionhttps://figshare.com/articles/software/FLIBase/23805993/2Other10.1093/NAR/GKAD74537697439PMC10767943Xianghuo Hexhhe@fudan.edu.cnhttps://orcid.org/0000-0003-4105-8674Person