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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software application, software toolkit, software resource, software library | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | 2026-08-04 09:43:09 | 77 | ||||||||
|
Gwyddion Resource Report Resource Website 1000+ mentions |
Gwyddion (RRID:SCR_015583) | data processing software, software application, software resource, data analysis software | Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry. | spm data analysis, spm data visualization, height field analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Czech Metrology Institute Department of Nanometrology | DOI:10.2478/s11534-011-0096-2 | Open source | OMICS_07548 | https://sources.debian.org/src/gwyddion/ | SCR_015583 | 2026-08-04 09:43:42 | 1510 | ||||||
|
PASA Resource Report Resource Website 500+ mentions |
PASA (RRID:SCR_014656) | data processing software, data analysis software, software resource, sequence analysis software, software application | Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute. | gene structure, annotation, gene structure analysis tool, spliced alignment, transcript sequence, bio.tools |
is used by: BRO_annotation is listed by: Debian is listed by: bio.tools |
DOI:10.1093/nar/gkg770 | Available for download | biotools:PASA | https://bio.tools/PASA | SCR_014656 | Program to Assemble Spliced Alignments (PASA), Program to Assemble Spliced Alignments | 2026-08-04 09:43:30 | 999 | ||||||
|
Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | data processing software, software application, software resource, workflow software | A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. | workflow, MD, molecular dynamics, simulation, software, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: bioKepler has parent organization: University of California at San Diego; California; USA |
NIGMS P41GM103426 | Requires Linux | biotools:ambergpumdsimulation | http://nbcr.ucsd.edu/data/downloads/workflows/, https://bio.tools/ambergpumdsimulation | SCR_014389 | Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation | 2026-08-04 09:43:25 | 1 | ||||||
|
tximport Resource Report Resource Website 50+ mentions |
tximport (RRID:SCR_016752) | data processing software, software application, software resource, data analysis software | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/, https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html, https://github.com/F1000Research/tximport, https://bio.tools/tximport | https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-08-04 09:43:59 | 91 | ||||
|
Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | data analysis service, analysis service resource, software resource, production service resource, service resource, web application | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele, https://bio.tools/nephele | SCR_016595 | 2026-08-04 09:43:56 | 27 | ||||||
|
ngsRelate Resource Report Resource Website 1+ mentions |
ngsRelate (RRID:SCR_016588) | data processing software, software application, software resource, data analysis software | Software tool for estimating pairwise relatedness from next-generation sequencing data. | estimating, pairwise, relatedness, next, generation, sequencing, data, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
Danish National Research Foundation ; Danish Council for Independent Research |
PMID:26323718 | Free, Available for download, Freely available | biotools:ngsRelateV2, biotools:ngsrelate | https://bio.tools/ngsRelateV2, https://bio.tools/ngsrelate | http://www.popgen.dk/software/index.php?title=NgsRelate&oldid=694 | SCR_016588 | ngsRelateV2 | 2026-08-04 09:43:56 | 6 | ||||
|
Computational Structural Biology Toolbox Resource Report Resource Website |
Computational Structural Biology Toolbox (RRID:SCR_016065) | CSB | software toolkit, software resource, software library | Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses. | software, library, Python, reading, storing, analysis, biomolecular, variety, statistical, analysis, bioinformatic |
is listed by: Debian is listed by: OMICtools |
Deutsche Forschungsgemeinschaft (DFG) grant HA 5918/1-1; Max Planck Society |
PMID:22942023 | Free, Available for download | OMICS_09827 | https://sources.debian.org/src/csb/ | SCR_016065 | Computational Structural Biology Toolbox (CSB), CSB Toolbox | 2026-08-04 09:43:48 | 0 | ||||
|
HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | data processing software, software application, software resource, workflow software | Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps. | Hi-C, data, raw, fastq, file, paired, Illumina, normalized, contact, map, bio.tools |
is listed by: Debian is listed by: bio.tools |
France Genomique National infrastructure ; Labex Deep ; European Research Coucil ; ERC Advanced Investigator award ; European Commission ; ABS4NGS project ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes ; Howard Hughes Medical Institute |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | 2026-08-04 09:44:12 | 206 | ||||||
|
OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data processing software, software application, software resource, data analysis software | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder | SCR_017118 | OrthoFinder2, OrthoFinder | 2026-08-04 09:44:04 | 2899 | |||||
|
scanpy Resource Report Resource Website 100+ mentions |
scanpy (RRID:SCR_018139) | data processing software, software application, software resource, data analysis software | Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time. | Large scale, single cell, gene expression, data analysis, R, pre processing, visualization, graph drawing, diffusion map, clustering, marker gene, differential expression test, bio.tools |
uses: BBKNN is used by: triku is used by: MUON is listed by: Debian is listed by: bio.tools is related to: Anndata has plug in: infercnvpy |
Helmholtz Postdoc Programme ; German Research Foundation |
PMID:29409532 | Free, Available for download, Freely available | biotools:scanpy, BioTools:scanpy | https://icb-scanpy.readthedocs-hosted.com/en/stable/, https://bio.tools/scanpy, https://bio.tools/scanpy, https://bio.tools/scanpy | SCR_018139 | Single Cell Analysis in Python | 2026-08-04 09:44:16 | 221 | |||||
|
Drop-seq tools Resource Report Resource Website 50+ mentions |
Drop-seq tools (RRID:SCR_018142) | data processing software, software application, software resource, data analysis software | Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript. | Simultaneous analysis, Drop-seq data, gene expression, thousands individual cells |
is listed by: Debian has parent organization: Broad Institute |
Stanley Center for Psychiatric Research ; MGH Psychiatry Residency Research Program ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award ; Simons Foundation ; NHGRI P50 HG006193; Klarman Cell Observatory ; NIMH U01 MH105960; NIMH R25 MH094612; NICHD F32 HD075541; NSF ECS 0335765; NSF DMR 1310266; NSF DMR 1420570 |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-08-04 09:44:16 | 94 | |||||||
|
DrivAER Resource Report Resource Website 1+ mentions |
DrivAER (RRID:SCR_019076) | data processing software, software application, software resource, data analysis software | Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data. | Manifold interpretation, scRNAseq data, relevance scores infering, transcriptional program, psuedotemporal ordering, disease status, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:drivaer | https://bio.tools/drivaer | SCR_019076 | Driving transcriptional programs using AutoEncoder based Relevance scores | 2026-08-04 09:44:28 | 1 | |||||||
|
Epigenomics Workflow on Galaxy and Jupyter Resource Report Resource Website 1+ mentions |
Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) | data processing software, data analysis software, workflow, software resource, training material, software application, narrative resource, data or information resource | Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. | Epigenomic, analysis, pipeline, ChIP-Seq, RNA-Seq, data, Galaxy, Jupyter, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Estatal de Investigación of Spain SEV-2016-0672 (2017-2021) | Free, Available for download, Freely available | biotools:Epigenomics_Workflow_on_Galaxy_and_Jupyter | https://zenodo.org/record/3298029, https://bio.tools/Epigenomics_Workflow_on_Galaxy_and_Jupyter | SCR_017544 | REA pipeline | 2026-08-04 09:44:09 | 2 | ||||||
|
IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | data processing software, portal, alignment software, analysis service resource, software resource, software application, image analysis software, production service resource, service resource, data or information resource | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHMRC ; MESR ; CNRS ; Université Montpellier 2 ; France ; GENCI |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-08-04 09:44:18 | 11 | |||||
|
PM4NGS Resource Report Resource Website 1+ mentions |
PM4NGS (RRID:SCR_019164) | data processing software, data analysis software, data management software, software resource, software application, workflow software, software toolkit | Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution. | NGS workflow, standard organizational structure generation, Next Generation Sequencing data, NGS data analysis, NGS data analysis workflow, data integration, Jupyter notebook, CWL format, bio.tools |
is listed by: bio.tools is listed by: Debian |
Intramural Research Program of the National Library of Medicine NIH | DOI:10.7490/f1000research.1117155.1 | Free, Freely available | biotools:pm4ngs | https://bio.tools/pm4ngs | SCR_019164 | Project Manager for Next Generation Sequencing | 2026-08-04 09:44:30 | 1 | |||||
|
ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data processing software, data analysis software, software resource, software application, data visualization software | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
German Cancer Research Center-Heidelberg Center for Personalized Oncology ; BMBF |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap, https://bio.tools/complexheatmap | SCR_017270 | 2026-08-04 09:44:07 | 3266 | ||||||
|
SWISS-MODEL Resource Report Resource Website 1000+ mentions |
SWISS-MODEL (RRID:SCR_018123) | web service, software resource, data access protocol, service resource, data or information resource | Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists. | 3D protein structure, homology modeling server, protein modeling, structural bioinformatics, automated comparative modeling, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: Swiss-PdbViewerDeepViewv4.0 has parent organization: University of Basel; Basel; Switzerland provides: SWISS-MODEL Repository |
PMID:12824332 | Free, Freely available | biotools:swiss-model_workspace, biotools:swiss_model | https://bio.tools/swiss_model, https://bio.tools/swiss-model_workspace | SCR_018123 | 2026-08-04 09:44:17 | 2796 | |||||||
|
SIGNOR Resource Report Resource Website 10+ mentions |
SIGNOR (RRID:SCR_018485) | storage service resource, data repository, service resource, database, data or information resource | Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles. | Signal transduction data, signaling information, published data collection, activity flow, chemical inhibitor, human proteome, manually annotated data, protein, protein relationship, FAIR data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: REDIportal |
Italian Association for Cancer Research ; ELIXIR-IIB ; Italian Node of the European ELIXIR infrastructure ; EMBL-EBI |
PMID:31665520 | Free, Available for download, Freely available | biotools:signor | https://bio.tools/signor | SCR_018485 | SIGnaling Network Open Resource, SIGNOR 2.0 | 2026-08-04 09:44:21 | 40 | |||||
|
OptiType Resource Report Resource Website 10+ mentions |
OptiType (RRID:SCR_022279) | data processing software, software application, software resource, data analysis software | Software tool for precision HLA typing from next generation sequencing data. | Precision HLA typing, next generation sequencing data, HLA typing, NGS data |
is listed by: Debian is listed by: OMICtools |
German Research Foundation ; German Federal Ministry of Education and Research |
PMID:25143287 | Free, Available for download, Freely available | OMICS_05461 | https://sources.debian.org/src/optitype/ | SCR_022279 | 2026-08-04 09:45:03 | 44 |
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