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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | data analysis software, data processing software, software application, software resource | Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcripto, assembler, RNAseq, data, short, read, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCRR P20 RR016460; NIGMS P20 GM103429; NSFC 61272016; NSFC 61432010 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | 2026-09-12 12:58:47 | 6 | ||||||
|
nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | JDRF ; NCI R33 CA225248; NIBIB R21 EB020976; NIDDK DP3 DK110844; NIDDK UC4 DK104167; NIGMS P41 GM103493; NIH Office Of The Director S10 OD016350 |
PMID:29491378 | SCR_017129 | 2026-09-12 12:58:48 | 1 | |||||||||
|
PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data access protocol, data or information resource, data repository, service resource, software resource, storage service resource, web service | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NHGRI U54 HG008097; NIGMS R01 GM103551; NIGMS R01 GM121696; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-09-12 12:58:49 | 0 | ||||||
|
CWL-Airflow Resource Report Resource Website 1+ mentions |
CWL-Airflow (RRID:SCR_017196) | CWL DAG | data processing software, software application, software resource, workflow software | Software Python package to extend Airflow functionality with Common Workflow Language support. Lightweight pipeline manager supporting Common Workflow Language. Can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on cloud platforms. | airflow, common workflow language, cwl, pipeline, workflow, docker | is listed by: OMICtools | NCATS UL1 TR001425; NIGMS DP2 GM119134 |
DOI:10.1101/249243 DOI:10.1093/gigascience/giz084 |
Free, Available for download, Freely available | OMICS_26560 | SCR_017196 | CWL-Airflow v 1.0.16, Common Workflow Language-Airflow | 2026-09-12 12:58:49 | 3 | |||||
|
FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data. | computing, theoretical, scattering, profile, structure, fitting, small, angle, X ray, data | has parent organization: University of California at San Francisco; California; USA | Lawrence Berkeley National Lab IDAT program ; NCRR U54 RR022220; NIGMS P41 GM109824; NIGMS R01 GM083960; NIGMS R01 GM105404; Rinat (Pfizer) Inc. ; Weizmann Institute Advancing Women in Science |
PMID:23972848 PMID:27151198 |
Free, Available for download, Freely available | SCR_017269 | Fast X-Ray Scattering | 2026-09-12 12:58:50 | 24 | |||||||
|
PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NHGRI HG005998; NIGMS P50 GM071508; NIGMS R01 GM071966 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-09-12 12:58:52 | 8 | ||||||||
|
microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | data processing software, image analysis software, image processing software, software application, software resource | Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing. | Image, guided, mass, spectrometry, automatic, cell, finding, point, based, registration, whole, slide, image, analysis, processing, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
National Science Foundation Graduate Research Fellowship Program ; NIDA DA018310; NIGMS T32 GM070421; NIMH U01 MH109062; Springborn Fellowship |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-09-12 12:58:53 | 1 | |||||||
|
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 | 2026-09-12 12:58:51 | 211 | |||||||
|
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 | 2026-09-12 12:58:54 | 6 | ||||||
|
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 | 2026-09-12 12:58:35 | 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 | 2026-09-12 12:58:35 | 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 | 2026-09-12 12:58:36 | 142 | |||||||||
|
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 | 2026-09-12 12:58:37 | 6 | |||||
|
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 | 2026-09-12 12:58:38 | 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 | 2026-09-12 12:58:44 | 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 | 2026-09-12 12:58:44 | 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 | 2026-09-12 12:58:44 | 25 | |||||||||
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FRETBursts Resource Report Resource Website 1+ mentions |
FRETBursts (RRID:SCR_016898) | FRETBursts | data analysis software, data processing software, software application, software resource, software toolkit | Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data. | freely, diffusing, single, molecule, FRET, smFRET, cellular, process, intermolecular, interaction, conformational, change, biomacromolecule, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM069709; NIGMS R01 GM95904 |
PMID:27532626 | Free, Available for download, Freely available | biotools:fretbursts | https://opensmfs.github.io/FRETBursts/, https://bio.tools/fretbursts | SCR_016898 | Förster Resonance Energy Transfer Bursts, FRETBursts | 2026-09-12 12:58:45 | 3 | ||||
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CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | data analysis software, data processing software, image analysis software, software application, software resource | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-09-12 12:58:45 | 18 | ||||||||
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ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | data analysis software, data processing software, software application, software resource | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIDA P30 DA018310; NIGMS R01 GM067193 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-09-12 12:58:45 | 14 |
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