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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
EMBL ; European Research Council ; Max Planck Society ; NIGMS U01 GM110749; Royal Society of New Zealand Marsden award ; Swiss National Science foundation |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-09-19 12:53:38 | 211 | |||||||
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Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, web service | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-09-19 12:53:43 | 6 | ||||||
|
Edtsurf Resource Report Resource Website 1+ mentions |
Edtsurf (RRID:SCR_016083) | data processing software, data visualization software, software application, software resource, source code | Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening. | construct, triangulate, surface, macromolecule, van der Waals, solvent, accessible, molecular, cavities, program |
is listed by: Debian is listed by: OMICtools |
NIGMS GM083107; NIGMS GM084222; NSF 0746198; the Alfred P. Sloan Foundation |
PMID:19956577 | Free, Available for download, Freely available | OMICS_16795 | https://sources.debian.org/src/edtsurf/ | SCR_016083 | EDTSurf: Quick and accurate construction of macromolecular surfaces | 2026-09-19 12:53:17 | 4 | |||||
|
fermi-lite Resource Report Resource Website 1+ mentions |
fermi-lite (RRID:SCR_016112) | algorithm resource, alignment software, data processing software, image analysis software, software application, software resource, standalone software | Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling. | assembling, short, read, small, region, sequencing, retain, heterozygous, event, diploid, variant, calling | is related to: Illumina | NHGRI U54 HG003037; NIGMS GM100233 |
PMID:26220959 | Free, Available for download | SCR_016112 | FermiKit, Fml-asm | 2026-09-19 12:53:17 | 4 | |||||||
|
Glam2 Resource Report Resource Website 100+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets. | motif, analysis, sequence, find, amino acid, nucleotide, set, alignment, gapped, recurring, variable, letnght, pattern, DNA, protein, output, discovery, dataset | is related to: MEME Suite - Motif-based sequence analysis tools | NIGMS R01 GM103544 | PMID:18437229 | Free, Freely available for non-commercial use | http://meme-suite.org/ | SCR_016129 | Glam2: Gapped local alignment of motifs 2 | 2026-09-19 12:53:18 | 203 | |||||
|
Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-09-19 12:53:19 | 142 | |||||||||
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ASHLAR Resource Report Resource Website 1+ mentions |
ASHLAR (RRID:SCR_016266) | Ashlar | data processing software, image processing software, software application, software resource | Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration. | cycif, registration, software, python, cyclic, immunofluorescence, fluorescence, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM107618 | Free, Available for download | biotools:ASHLAR | https://bio.tools/ASHLAR | SCR_016266 | ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration | 2026-09-19 12:53:20 | 6 | |||||
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lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction. | personalized, medicine, metabolomics, data, classification, clustering, biomarker, prediction, algorithm, calculating, microarray, enrichment |
is listed by: OMICtools is related to: University of Hawaii; Hawaii; USA |
NICHD R01 HD084633; NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-09-19 12:53:21 | 3 | |||||||
|
Leginon Resource Report Resource Website 10+ mentions |
Leginon (RRID:SCR_016731) | data acquisition software, data or information resource, data processing software, data repository, image acquisition software, portal, service resource, software application, software resource, storage service resource | System designed for automated collection of images from a transmission electron microscope. | automated, collection, acquisition, data, image, electron, microscope |
uses: Python Programming Language has parent organization: Scripps Research Institute |
NCRR RR17573; NIGMS GM61939; NSF DBI0352386; NSF DBI9730056; NSF DBI9904547 |
PMID:15890530 | Free, Available for download, Freely available, Registration suggested | SCR_016731 | 2026-09-19 12:53:28 | 45 | ||||||||
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PMI-Byonic Resource Report Resource Website 10+ mentions |
PMI-Byonic (RRID:SCR_016735) | Byonic | data analysis software, data processing software, software application, software resource | Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type. | Byonic, Protein Metrics Inc., peptide, protein, identification, mass, spectrometry | NIGMS R21 GM085718 | PMID:23255153 | Commercially available | SCR_016735 | Protein Metrics Inc. Byonic, PMI-Byonic, PMI Byonic, Byonic | 2026-09-19 12:53:28 | 25 | |||||||
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PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | data analysis software, data processing software, software application, software resource | Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype. | detect, gene, disease, associate, trait, mechanism, molecular, variation, phenotype | NCI F32CA165823; NCI K12 CA139160; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595; NIGMS U01 GM092691; NIGMS U01 GM61393; NIMH P50 MH094267; NIMH R01 MH090937; NIMH R01 MH101820; NIMH T32 MH020065 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | 2026-09-19 12:53:28 | 25 | |||||||||
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TFmodeller Resource Report Resource Website 1+ mentions |
TFmodeller (RRID:SCR_015715) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, web application | Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs. | protein-dna complex, comparative model, modeling software, schematic interface diagram, interface alignment, dna motif, complex coordinate | NIGMS RO1-GM071962 | PMID:17459960 | Free for academic use, Freely available, Tutorial available | http://maya.ccg.unam.mx/~tfmodell/ | SCR_015715 | 2026-09-19 12:53:11 | 1 | ||||||||
|
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 | GENE Expression and Enrichment Vector Analyzer | 2026-09-19 12:53:10 | 5 | |||||
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CRowd Extracted Expression of Differential Signatures Resource Report Resource Website 1+ mentions |
CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) | CREEDS | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures. | variant, disease expression, disease marker | NIGMS R01GM098316; NHLBI U54HL127624; NCI U54CA189201 |
PMID:27667448 | Freely available, Free, Available for download | SCR_015680 | CREEDS: CRowd Extracted Expression of Differential Signatures | 2026-09-19 12:53:10 | 6 | |||||||
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NeuroExpresso Resource Report Resource Website 10+ mentions |
NeuroExpresso (RRID:SCR_015724) | data or information resource, database, software resource, web application | Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. | mouse brain, marker gene, tissue expression, microarray, gene expression, rna sequencing | NeuroDevNet ; CAMH ; NIMH MH077159; NIMH MH111099; NIGMS 719GM076990; NSERC Discovery Grant |
Freely available | https://github.com/oganm/neuroexpresso | SCR_015724 | 2026-09-19 12:53:11 | 26 | |||||||||
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Rosetta Resource Report Resource Website 100+ mentions |
Rosetta (RRID:SCR_015701) | simulation software, software application, software resource, software toolkit | Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. | Molecular modeling, structure prediction, computational modeling, protein analysis, enzyme design, macromolecular complexes |
is used by: trRosetta is related to: PyRosetta works with: ROSIE |
Hertz Foundation Fellowship ; NCI F32 CA189246; NIGMS GM078221; NIGMS GM084453; NIGMS GM092802; NIGMS GM110089; NIGMS GM111819; NIGMS GM114961; NIGMS GM117189; NIGMS GM73141; NSF Graduate Research Fellowship ; NSF BMAT 1507736; Simons Foundation |
PMID:28430426 PMID:21829626 PMID:18442991 |
Restricted | SCR_015701 | Rosetta modeling software | 2026-09-19 12:53:11 | 216 | |||||||
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CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI R00 HG008399; NHGRI R01 HG005085; NHGRI RM1 HG009490; NHLBI P01 HL32262; NHLBI R01 HL119099; NIBIB R01 EB022376; NIDDK P30 DK049216; NIDDK R03 DK109232; NIGMS R35 GM118062; NIGMS R35 GM118158 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2, https://github.com/pinellolab/CRISPResso | SCR_021538 | CRISPResso2 | 2026-09-19 12:54:54 | 27 | |||||||
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RepEnrich Resource Report Resource Website 10+ mentions |
RepEnrich (RRID:SCR_021733) | data analysis software, data processing software, software application, software resource | Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data. | profile enrichment, next generation sequencing reads, transposable elements, estimate repetitive element enrichment, genome wide transcriptional regulation, sequencing data | has parent organization: Brown University; Rhode Island; USA | NIA K25 AG028753; NIA R37 AG016694; NIGMS T32 GM007601 |
PMID:25012247 | Free, Available for download, Freely available | https://github.com/nerettilab/RepEnrich2 | SCR_021733 | RepEnrich2 | 2026-09-19 12:54:57 | 21 | ||||||
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DeepCell Resource Report Resource Website 10+ mentions |
DeepCell (RRID:SCR_022197) | data processing software, image analysis software, segmentation software, software application, software resource | Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software. | segmenting individual cells, microscopy image, cell segmentation | NIGMS F32 GM119319; NIGMS P50 GM107615; NLM DP1 LM01150; Paul Allen Family Foundation |
DOI:10.1371/journal.pcbi.1005177 | Free, Available for download, Freely available | SCR_022197 | Deepcell | 2026-09-19 12:55:03 | 14 | ||||||||
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Modeling Infectious Disease Agents Study online portal for COVID-19 Resource Report Resource Website 1+ mentions |
Modeling Infectious Disease Agents Study online portal for COVID-19 (RRID:SCR_018281) | data or information resource, portal, topical portal | Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases. | COVID-19, COVID-19 data, modeling research, public data, metadata, infectious disease | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | NIGMS | Free, Freely available | https://github.com/midas-network/COVID-19 | SCR_018281 | MIDAS online portal for COVID-19 | 2026-09-19 12:53:49 | 4 |
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