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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Bio2BEL Resource Report Resource Website 1+ mentions |
Bio2BEL (RRID:SCR_017659) | software toolkit, software resource | Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications. | Biological, expression, language, integration, layer, dataset, biological, database |
uses: PyBEL is listed by: Debian is listed by: bio.tools is related to: Biological Expression Language |
DOI:10.1101/631812 | Free, Available for download, Freely available | biotools:bio2bEL, BioTools:Bio2BEL | https://github.com/bio2bel/bio2bel, https://bio.tools/Bio2BEL, https://bio.tools/Bio2BEL | SCR_017659 | 2026-08-02 09:07:52 | 7 | |||||||
|
viridis Resource Report Resource Website 10+ mentions |
viridis (RRID:SCR_016696) | software toolkit, software resource | Software package which brings to R color scales. Created for the Python matplotlib library. | R, color, scale, Python, matplotlib, CRAN |
is affiliated with: R Project for Statistical Computing is affiliated with: CRAN |
Free, Available for download, Freely available | https://github.com/sjmgarnier/viridis | SCR_016696 | 2026-08-02 09:07:21 | 27 | |||||||||
|
Protein Prospector Resource Report Resource Website 500+ mentions |
Protein Prospector (RRID:SCR_014558) | software toolkit, software resource | A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass. | database search program, database search, database management, peptide, protein, mass spectrometry, ms, utility program, batch msms, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
Open source, Freely available to academic researchers | biotools:proteinprospector | https://bio.tools/proteinprospector | SCR_014558 | ProteinProspector | 2026-08-02 09:06:57 | 569 | |||||||
|
ACD/ NMR Processor Resource Report Resource Website |
ACD/ NMR Processor (RRID:SCR_014679) | software toolkit, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports. | metabolomics, metabolomics tool, structure verification, data analysis, nmr, nmr processing | is listed by: Metabolomics Workbench | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014679 | 2026-08-02 09:07:02 | 0 | ||||||||||
|
kb_python Resource Report Resource Website 10+ mentions |
kb_python (RRID:SCR_018213) | software toolkit, software resource | Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.). | Wrapper, single cell RNA seq, pre-processing, species specific index, pseudo alignment, read, gene count matrice, RNA velocity analysis, data |
works with: kallisto works with: Bustools |
DOI:10.1038/nbt.3519 DOI:10.1101/673285 |
Free, Available for download, Freely available | SCR_018213 | 2026-08-02 09:07:42 | 16 | |||||||||
|
TreeBeST Resource Report Resource Website 50+ mentions |
TreeBeST (RRID:SCR_018173) | software toolkit, software resource | Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate. | Phylogenetic tree, gene tree, phylogeny | Free, Available for download, Freely available | SCR_018173 | NJTREE, Tree Building guided by Species Tree | 2026-08-02 09:07:40 | 67 | ||||||||||
|
peppy Resource Report Resource Website 1+ mentions |
peppy (RRID:SCR_021078) | software toolkit, software resource | Software python package for reading Portable Encapsulated Projects or PEPs in python. | reading Portable Encapsulated Projects, PEPs, python |
is related to: eido is related to: pepr |
DOI:10.1101/2020.10.08.331322 | Free, Available for download, Freely available | http://peppy.databio.org/en/latest/, https://github.com/pepkit/peppy/ | SCR_021078 | 2026-08-02 09:08:04 | 2 | ||||||||
|
PhaseME Resource Report Resource Website 1+ mentions |
PhaseME (RRID:SCR_018739) | software toolkit, software resource | Software tool set to assess quality of per read phasing information and help to reduce errors during this process. | Variant Call Format Tools, quality assessment, read phasing, error, reduce error, read phasing information, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:phaseme | https://bio.tools/phaseme/ | SCR_018739 | 2026-08-02 09:08:00 | 1 | ||||||||
|
QuickFigures Resource Report Resource Website 1+ mentions |
QuickFigures (RRID:SCR_019082) | software toolkit, software resource | Software package to quickly transform microscope images into quality figures. User friendly tool for creating and formatting scientific figures, can export files into popular softwares like Adobe Illustrator, Microsoft Powerpoint, and Inkscape. | Transform microscope image, creating scientific figure, formatting scientific figure, quality fiqure | is a plug in for: ImageJ | DOI:10.1101/2020.09.24.311282 | SCR_019082 | 2026-08-02 09:07:56 | 1 | ||||||||||
|
ProtHint Resource Report Resource Website 10+ mentions |
ProtHint (RRID:SCR_021167) | software toolkit, software resource | Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences. | Predicting and scoring hints, form of introns, start and stop codons, genome, mapping, spliced aligning, predicted genes, database, reference protein sequences | has parent organization: Georgia Institute of Technology; Georgia; USA | Free, Available for download, Freely available | SCR_021167 | 2026-08-02 09:08:05 | 45 | ||||||||||
|
r8s Resource Report Resource Website 10+ mentions |
r8s (RRID:SCR_021161) | software toolkit, software resource | Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies. | Divergence time estimation, phylogenies, estimating absolute rates, molecular evolution, divergence times, phylogenetic tree | Free, Available for download, Freely available | SCR_021161 | 2026-08-02 09:08:05 | 13 | |||||||||||
|
Artistoo Resource Report Resource Website 1+ mentions |
Artistoo (RRID:SCR_020983) | software toolkit, software resource | Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser. | Cellular Potts Models, simulation models building, cells simulation models, tissue simulation models, JavaScript library, build interactive models | DOI:10.1101/2020.05.01.072975 | Free, Freely available | biotools:artistoo | https://github.com/ingewortel/artistoo, https://bio.tools/artistoo | SCR_020983 | Artificial Tissue Toolbox | 2026-08-02 09:08:02 | 2 | |||||||
|
Conda Resource Report Resource Website 50+ mentions |
Conda (RRID:SCR_018317) | software toolkit, software resource | Software tool as cross platform, language agnostic binary package manager. Open source package management system and environment management system that runs on Windows, macOS and Linux. Can quickly install, run, and update packages and their dependencies. Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Created for Python programs, but it can package and distribute software for any language. Conda can be combined with continuous integration systems such as Travis CI and AppVeyor to provide frequent, automated testing of your code. Conda package and environment manager is included in all versions of Anaconda and Miniconda. | Package manager system, environment management system, software distribution, integration system, automated code testing |
is related to: BioConda is related to: RNAProt |
Free, Available for download, Freely available | https://conda.io/, https://github.com/conda/conda | SCR_018317 | 2026-08-02 09:07:56 | 93 | |||||||||
|
cvequality Resource Report Resource Website 1+ mentions |
cvequality (RRID:SCR_019124) | software toolkit, software resource | Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations. | testing significant differences, coefficients of variation, multiple groups | is listed by: CRAN | Free, Available for download, Freely available | https://CRAN.R-project.org/package=cvequality | SCR_019124 | 2026-08-02 09:08:05 | 2 | |||||||||
|
gtsummary Resource Report Resource Website 1+ mentions |
gtsummary (RRID:SCR_021319) | software toolkit, software resource | Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables. | Publication ready data summary, customizable presentation ready tables, summarizing data sets, regression models, creating presentation ready data tables, data tables, data summary | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/ddsjoberg/gtsummary | SCR_021319 | 2026-08-02 09:08:08 | 9 | |||||||||
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GWAS Quality Control Pipeline Resource Report Resource Website 1+ mentions |
GWAS Quality Control Pipeline (RRID:SCR_019241) | software toolkit, software resource | Software tool as scalable GWAS Quality Control pipeline for biobank scale datasets. | GWAS, data quality control, biobank scale datasets, genome wide association study | is related to: GWASdb | Free, Available for download, Freely available | SCR_019241 | BIGwas QC | 2026-08-02 09:08:07 | 3 | |||||||||
|
PRISMA2020 Resource Report Resource Website 10+ mentions |
PRISMA2020 (RRID:SCR_021053) | software toolkit, software resource | Software R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams. ShinyApp for producing PRISMA 2020 compliant flow diagrams. | PRISMA 2020 compliant flow diagrams, producing flow diagrams, ShinyApp | Free, Available for download, Freely available | https://github.com/nealhaddaway/PRISMA2020/tree/0.0.1, https://zenodo.org/record/4287835#.YGyXuuhKhPZ | SCR_021053 | 2026-08-02 09:08:10 | 25 | ||||||||||
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plyranges Resource Report Resource Website 1+ mentions |
plyranges (RRID:SCR_021324) | software toolkit, software resource | Open source software R package for interacting with common Bioconductor classes Ranges and GenomicRanges. Grammar of genomic data transformation. Provides grammatical and consistent way of manipulating these classes to increase accessiblity for new Bioconductor users. | genomic data transformation, genomic data transformation grammar, genomic data, data transformation, | DOI:10.1186/s13059-018-1597-8 | Free, Available for download, Freely available | https://github.com/sa-lee/plyranges | SCR_021324 | 2026-08-02 09:08:08 | 1 | |||||||||
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ChIPseeker Resource Report Resource Website 100+ mentions |
ChIPseeker (RRID:SCR_021322) | software toolkit, software resource | Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes. | Retrieve nearest genes around peak, annotate genomic region of peak, overlap estimate significance, ChIP peak data sets |
uses: Gene Expression Omnibus (GEO) is listed by: Bioconductor |
PMID:25765347 | Free, Available for download, Freely available | SCR_021322 | 2026-08-02 09:08:08 | 290 | |||||||||
|
SeqKit Resource Report Resource Website 100+ mentions |
SeqKit (RRID:SCR_018926) | software toolkit, software resource | Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation. | FASTA file, Q file, file manipulation, fast toolkit | DOI:10.1371/journal.pone.0163962 | Free, Available for download, Freely available | https://github.com/shenwei356/seqkit | SCR_018926 | 2026-08-02 09:08:02 | 154 |
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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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