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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ggplot2 Resource Report Resource Website 10000+ mentions |
ggplot2 (RRID:SCR_014601) | data processing software, data visualization software, software application, software resource | Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers. | plotting system, r, graphics, data analysis, multi-layered graphics, bio.tools |
uses: ggpubr uses: ggeffects uses: ggsignif is used by: riboWaltz is used by: ClustVis is used by: ggrepel is used by: PlotsOfData is used by: EnhancedVolcano is used by: tidyverse is used by: ComplexUpset is used by: ggfortify is used by: forestmodel is used by: ggvenn is used by: metaviz is used by: ggVennDiagram is used by: ggcyto is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: ggraph is related to: ggbiplot is related to: GGally is related to: ggstatsplot is related to: ggpointdensity has parent organization: CRAN works with: Plotly works with: cowplot works with: ggalluvial works with: ggforce works with: ggbreak works with: ggrastr works with: tidybayes works with: ggsurvfit works with: ggtext works with: ggsci |
Free, Freely available | biotools:ggplot2 | http://docs.ggplot2.org/current/, https://github.com/tidyverse/ggplot2, https://bio.tools/ggplot2 | http://ggplot2.org/ | SCR_014601 | SciCrunch Registry | grammar of graphics plot2 | 2026-09-28 09:33:16 | 42192 | ||||||
|
Metastats Resource Report Resource Website 100+ mentions |
Metastats (RRID:SCR_014610) | data analysis software, data processing software, software application, software resource, web application | A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test. | microbiome, statistics, software, metagenomics, clinical data, data analysis software, machine learning, web application, bio.tools |
is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian |
Open source, Acknowledgement requested | biotools:metastats | https://bio.tools/metastats | SCR_014610 | SciCrunch Registry | 2026-09-26 02:15:27 | 390 | ||||||||
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OpenWorm Resource Report Resource Website 10+ mentions |
OpenWorm (RRID:SCR_014650) | simulation software, software application, software resource, web application | 3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders. | simulation, model, web application, web browser, c elegans, nematode, worm, roundworm, open source, 3d, dissect, anatomy, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: WormBase is hosted by: GitHub |
PMID:25404913 DOI:10.3389/fncom.2014.00137 |
Open source, Code is available on GitHub, Available on the App Store | SCR_014984, biotools:OpenWorm | https://bio.tools/OpenWorm | SCR_014650 | SciCrunch Registry | OpenWorm Browser, Open Worm | 2026-09-26 02:15:28 | 21 | ||||||
|
FluoRender Resource Report Resource Website 100+ mentions |
FluoRender (RRID:SCR_014303) | data analysis software, data processing software, data visualization software, software application, software resource | Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation. | rendering tool, confocal microscopy data visualization, neurobiology, fluorescent stain, brain, bio.tools |
is used by: VVD Viewer is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
Free, Available for download, Freely available | biotools:fluorender | https://bio.tools/fluorender | SCR_014303 | SciCrunch Registry | FluoRender Visualization | 2026-09-26 02:15:24 | 130 | |||||||
|
NiftyFit Resource Report Resource Website 10+ mentions |
NiftyFit (RRID:SCR_014301) | software library, software resource, software toolkit | Software package for multi-parametric model-fitting of 4D Magnetic Resonance Imaging data. Software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI. T | software library, voxel wise fit, relaxometry, mri, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University College London; London; United Kingdom |
EPSRC ; MRC ; NIHR BRC ; NIHR |
PMID:26972806 | Free, Available for download, Freely available | biotools:niftyfit, BioTools:niftyfit | https://github.com/KCL-BMEIS/niftyreg, https://bio.tools/niftyfit, https://bio.tools/niftyfit, https://bio.tools/niftyfit | SCR_014301 | SciCrunch Registry | 2026-09-26 02:15:24 | 14 | ||||||
|
ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | data analysis software, data processing software, software application, software resource, web application | Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, model, best fit model, protein evolution, amino acid replacement, server, bio.tools |
uses: PhyML is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is hosted by: GitHub |
PMID:15647292 DOI:10.1093/bioinformatics/btr088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11547, biotools:prottest | https://github.com/ddarriba/prottest3, https://bio.tools/prottest, https://sources.debian.org/src/prottest/ | SCR_014628 | SciCrunch Registry | 2026-09-26 02:15:27 | 1984 | |||||||
|
FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | software resource, web application | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | SciCrunch Registry | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-09-26 02:15:28 | 139 | |||||
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SortMeRNA Resource Report Resource Website 500+ mentions |
SortMeRNA (RRID:SCR_014402) | data analysis software, data processing software, sequence analysis software, software application, software resource | Sequence analysis software for filtering, mapping and OTU-picking NGS reads. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis software, filter, map, otu picking, ngs, sort, rna, rrna, bio.tools |
uses: QIIME is listed by: Debian is listed by: bio.tools |
PMID:23071270 DOI:10.1093/bioinformatics/bts611 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02619, biotools:sortmerna | https://bio.tools/sortmerna, https://sources.debian.org/src/sortmerna/ | SCR_014402 | SciCrunch Registry | 2026-09-26 02:15:25 | 624 | |||||||
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CummeRbund Resource Report Resource Website 100+ mentions |
CummeRbund (RRID:SCR_014568) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions. | r software, cufflink, rna-seq, sqlite, gene, transcript, transcription start site, cds region, r, rnaseq, rna seq, bio.tools, FASEB list |
uses: R Project for Statistical Computing is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard University; Cambridge; United States |
Free, Freely available | biotools:cummerbund, OMICS_07349 | https://bio.tools/cummerbund, https://sources.debian.org/src/r-bioc-cummerbund/ | SCR_014568 | SciCrunch Registry | 2026-09-26 02:15:27 | 366 | ||||||||
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FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | data analysis software, data management software, data processing software, software application, software resource | Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis. | quality control, sequence data, sequencing, analysis, data quality, pipeline, raw sequence data, modular set, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Open source, Available for download | biotools:fastqc, SCR_005539, OMICS_01043 | https://omictools.com/fastqc-tool, https://bio.tools/fastqc, https://sources.debian.org/src/fastqc/ | SCR_014583 | SciCrunch Registry | FastQC v0.11.5 | 2026-09-26 02:15:27 | 19827 | |||||||
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Mascot Resource Report Resource Website 5000+ mentions |
Mascot (RRID:SCR_014322) | data processing software, signal processing software, software application, software resource, standalone software | A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters. | server, software package, mass spectrometry, protein, identify, characterize, bio.tools |
is used by: MSQuant is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MascotScan |
Free, Can be licensed for in-house use, Available for download | biotools:MASCOT | http://www.matrixscience.com/search_intro.html, https://bio.tools/MASCOT | SCR_014322 | SciCrunch Registry | Mascot Server | 2026-09-26 02:15:24 | 7141 | |||||||
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GROMACS Resource Report Resource Website 5000+ mentions |
GROMACS (RRID:SCR_014565) | simulation software, software application, software resource, software toolkit | Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers. | simulation, molecular dynamics, software package, software toolkit, biochemical, molecule, protein, lipid, nucleic acid, bond interaction, bio.tools |
is used by: CHARMM-GUI is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ; Nvidia ; Stream Computing Performance Engineers ; Swedish eScience Research Center ; Swedish Foundation for International Cooperation in Research and Higher Education ; Swedish Foundation for Strategic Research ; Swedish National Infrastructure for Computing ; Swedish Research Council |
PMID:26620784 DOI:10.1016/0010-4655(95)00042-E |
Free, Available for download | biotools:gromacs, OMICS_05081 | https://bio.tools/gromacs, https://sources.debian.org/src/gromacs/, https://github.com/gromacs/gromacs | SCR_014565 | SciCrunch Registry | Gromacs | 2026-09-26 02:15:27 | 9367 | |||||
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GEMINI Resource Report Resource Website 500+ mentions |
GEMINI (RRID:SCR_014819) | software resource | Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD. | framework, genetic variation, annotation, human, genome, vcf, database, , bio.tools, FASEB list |
uses: KEGG uses: ENCODE uses: OMIM uses: dbSNP uses: HPRD - Human Protein Reference Database is listed by: Debian is listed by: bio.tools has parent organization: University of Utah; Utah; USA |
DOI:10.1371/journal.pcbi.1003153 | Freely available | biotools:gemini | https://github.com/arq5x/gemini, https://bio.tools/gemini | SCR_014819 | SciCrunch Registry | GEnome MINIng (GEMINI), GEMINI - a flexible framework for exploring genome variation, Genome Mining, GEnome MINIng | 2026-09-26 02:15:29 | 532 | ||||||
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PAML Resource Report Resource Website 1000+ mentions |
PAML (RRID:SCR_014932) | PAML | data analysis software, data processing software, software application, software resource, software toolkit | Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic analysis, dna, protein sequences, evolutionary process, estimate parameters, test hypothesis, maximum likelihood, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Berkeley; Berkeley; USA works with: PAUP works with: PHYLIP works with: PhyML works with: RAxML |
PMID:9367129 DOI:10.1093/molbev/msm088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04238, biotools:paml | https://bio.tools/paml, https://sources.debian.org/src/paml/ | SCR_014932 | SciCrunch Registry | Phylogenetic Analysis by Maximum Likelihood, Phylogenetic Analysis by Maximum Likelihood (PAML) | 2026-09-26 02:15:30 | 4962 | |||||
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CHiCAGO Resource Report Resource Website 100+ mentions |
CHiCAGO (RRID:SCR_014941) | data analysis software, data processing software, software application, software resource, software toolkit | Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | capture hi-c, capture hi-c data, chic, brownian collisions, chromatin, p-value weighting, genomic organization, genome, statistical analysis, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
BBSRC ; MRC UK ; EMBL |
PMID:27306882 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:chicago | https://bitbucket.org/chicagoTeam/chicago, https://bio.tools/chicago | SCR_014941 | SciCrunch Registry | Capture HiC Analysis of Genomic Organisation, Capture HiC Analysis of Genomic Organization, CHiCAGO: Capture HiC Analysis of Genomic Organisation | 2026-09-26 02:15:30 | 163 | |||||
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SOAPnuke Resource Report Resource Website 1000+ mentions |
SOAPnuke (RRID:SCR_015025) | data analysis software, data processing software, sequence analysis software, software application, software resource | Multi-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status. | sequence data, fastq, dge dataset, rna, metagenomics, bio.tools |
is listed by: SOAP is listed by: bio.tools is listed by: Debian |
Open Source, Free | biotools:soapnuke | https://bio.tools/soapnuke | SCR_015025 | SciCrunch Registry | 2026-09-26 02:15:31 | 1698 | ||||||||
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Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 | SCR_016368 | SciCrunch Registry | , bowtie 2, bowtie2 v 2.2.3 | 2026-09-26 02:15:28 | 1993 | |||||
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MetaMapR Resource Report Resource Website 1+ mentions |
MetaMapR (RRID:SCR_014685) | data processing software, data visualization software, software application, software resource | An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques. | metabolomics, metabolomics tool, enzymatic transformations, metabolite structural similarity, mass spectral similarity, metabolic networks, data visualization, bio.tools |
is listed by: Metabolomics Workbench is listed by: Debian is listed by: bio.tools |
PMID:25847005 | Open source | biotools:metamapr | https://bio.tools/metamapr | SCR_014685 | SciCrunch Registry | 2026-09-26 02:15:28 | 9 | |||||||
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GEN3VA Resource Report Resource Website 1+ mentions |
GEN3VA (RRID:SCR_015682) | data analysis software, data processing software, software application, software resource | Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme. | GEO2Enrichr, gene expression signatures, enrichment analyses, multiple studies, biological theme, bio.tools |
is listed by: bio.tools is listed by: Debian works with: Gene Expression Omnibus (GEO) |
NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27846806 | Free, Freely available | biotools:gen3va | https://github.com/MaayanLab/gen3va, https://bio.tools/gen3va | SCR_015682 | SciCrunch Registry | GENE Expression and Enrichment Vector Analyzer | 2026-09-26 02:15:35 | 5 | |||||
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Off-Spotter Resource Report Resource Website 50+ mentions |
Off-Spotter (RRID:SCR_015739) | algorithm resource, software resource, web application | Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers. | CRISPR, Cas, sgrna, prokaryotic immune system, genetic engineering, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Thomas Jefferson University; Pennsylvania; USA |
William M. Keck Foundation | PMID:25630343 | Freely available, Free, Available for download, Tutorial available | biotools:off-spotter | https://bio.tools/off-spotter | SCR_015739 | SciCrunch Registry | Off-Spotter: tool for CRISPR/Cas design, Off-spotter sgRNA algorithm | 2026-09-26 02:15:36 | 53 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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