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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | software application, data processing software, software resource | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-02-17 10:00:10 | 5 | |||||
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Short Time-series Expression Miner (STEM) Resource Report Resource Website 50+ mentions |
Short Time-series Expression Miner (STEM) (RRID:SCR_005016) | STEM | software application, data processing software, software resource | The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | statistical analysis, term enrichment, visualization, cluster, compare, short time series, gene expression, microarray, expression profile, gene, gene ontology, gene enrichment analyses, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Carnegie Mellon University; Pennsylvania; USA |
NIAID NO1 AI-5001; NSF 0448453 |
PMID:16597342 PMID:15961453 |
Open unspecified license - Free for academic use | nlx_97053 | SCR_005016 | Short Time-series Expression Miner | 2026-02-17 10:00:43 | 81 | |||||
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Ontodog: A Web-based Ontology View Generator Resource Report Resource Website 10+ mentions |
Ontodog: A Web-based Ontology View Generator (RRID:SCR_005061) | Ontodog | production service resource, source code, service resource, software resource | Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0. | ontology, interoperability | has parent organization: University of Michigan Medical School; Michigan; USA | Rackham Pilot Research ; NIAID R01AI081062; NIGMS 5R01GM93132-1 |
nlx_144053 | SCR_005061 | 2026-02-17 10:00:43 | 17 | ||||||||
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SALSA Resource Report Resource Website 10+ mentions |
SALSA (RRID:SCR_022013) | data analysis software, software application, data processing software, software resource | Software tool for scaffold long read assemblies with Hi-C data. | scaffolding, Hi-C data, scaffold long read assemblies | NHGRI R44 HG009584; NIAID R01 AI100947; Ministry of Health and Welfare ; Republic of Korea |
DOI:10.1371/journal.pcbi.1007273 DOI:10.1186/s12864-017-3879-z |
Free, Available for download, Freely available | SCR_022013 | SALSA2 | 2026-02-17 10:04:07 | 40 | ||||||||
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Stitchr Resource Report Resource Website 1+ mentions |
Stitchr (RRID:SCR_022139) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information. | Stitch together coding TCR nucleotide sequences, Python, T cell receptors nucleotide, V and J gene symbols, hypervariable CDR3 amino acid sequence, fully spliced TCR cDNA | NCI R01 CA164273; NIAID R43 AI120313; NCI R43 CA232942; Emily Venanzi Fund |
PMID:35325179 | Free, Available for download, Freely available | SCR_022139 | 2026-02-17 10:04:08 | 3 | |||||||||
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Harmony Resource Report Resource Website 100+ mentions |
Harmony (RRID:SCR_022206) | data analysis software, software application, data processing software, software resource | Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data. | cells grouping, cell type, experimental factors, biological factors, single cell data integration | is used by: harmonypy | NIAID U19 AI111224; NIH R01 AR063759; NIH UH2 AR067677; NIH T32 AR007530 |
PMID:31740819 | Free, Available for download, Freely available | SCR_022206 | Harmony for immunogenomics | 2026-02-17 10:03:34 | 171 | |||||||
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MCScanX Resource Report Resource Website 100+ mentions |
MCScanX (RRID:SCR_022067) | software application, data processing software, data analysis software, software resource, software toolkit | Software toolkit for detection and evolutionary analysis of gene synteny and collinearity. | gene synteny and collinearity, detection and evolutionary analysis, | NSF DBI 0849896; NSF MCB 0821096; NSF MCB 1021718; NIAID R01 AI068908 |
PMID:22217600 | Free, Available for download, Freely available | SCR_022067 | Multiple Collinearity Scan toolkit X version | 2026-02-17 10:04:08 | 257 | ||||||||
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National Swine Resource and Research Center Resource Report Resource Website 50+ mentions |
National Swine Resource and Research Center (RRID:SCR_006855) | NSRRC | organism supplier, biomaterial supply resource, cell repository, material resource | Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. | RIN, Resource Information Network, pig, fetal fibroblast, live animal, tissue, fibroblast, fetus, genetically modified pig, biomaterial manufacture, genome, genotyping, genetics, reproduction, breeding, health monitoring, cryopreservation, phenotyping, consulting, RRID Community Authority |
is used by: Integrated Animals is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: One Mind Biospecimen Bank Listing has parent organization: University of Missouri; Missouri; USA |
NIH Office of the Director U42 OD011140; NIAID ; NHLBI |
Public, To investigators, Application required | nif-0000-12086 | SCR_006855 | National Swine Resource Research Center | 2026-02-17 10:01:10 | 79 | ||||||
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Tracer Resource Report Resource Website 1000+ mentions |
Tracer (RRID:SCR_019121) | software application, data processing software, data analysis software, software resource, data visualization software | Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. | Analysing trace files, files generated by Bayesian MCMC runs, MCMC trace files, conditional posterior distribution summary, demographic trajectory reconstruction, Bayesian phylogenetic inference, kernel density estimation, multivariate visualisation | Wellcome Trust ; European Union Seventh Framework Programme ; NSF DMS 1264153; NIAID R01 AI107034; NIAID U19 AI135995 |
PMID:29718447 | Free, Available for download, Freely available | https://github.com/beast-dev/tracer http://gensoft.pasteur.fr/docs/Tracer/v1.6 http://beast.community/tracer https://github.com/beast-dev/tracer/releases/tag/v1.7.1 |
SCR_019121 | Tracer v1.7.1, Tracer v1.6 | 2026-02-17 10:03:37 | 1582 | |||||||
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ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | software application, data processing software, data analysis software, software resource, software toolkit | Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing. | single-cell ATAC-seq data analysis, single-cell ATAC-seq data processing, single cell chromatin accessibility analysis, doublet removal, single cell clustering, cell type identification, unified peak set generation, cellular trajectory identification, transcription factor footprinting | NHGRI RM1 HG007735; NHGRI UM1 HG009442; NCI R35 CA209919; NHGRI UM1 HG009436; NCI U2C CA233311; NIAID U19 AI057266; NIA K99 AG059918; American Society of Hematology Scholar Award ; International Collaborative Award ; Defense Advanced Research Project Agency ; Ray and Dagmar Dolby Family Fund ; Stanford Cancer Institute-Goldman Sachs Foundation Cancer Research Award |
PMID:33633365 | Free, Available for download, Freely available | https://github.com/GreenleafLab/ArchR https://www.archrproject.com/ https://github.com/GreenleafLab/ArchR_2020 |
SCR_020982 | 2026-02-17 10:03:55 | 358 | ||||||||
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DatA Tag Suite Resource Report Resource Website |
DatA Tag Suite (RRID:SCR_019236) | DATS | narrative resource, data or information resource, software resource, software toolkit, standard specification | Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex. | Data processing, data discovery, metadata submission, DataMed, data, discovery | NIAID U24 AI117966; ELIXIR EXCELERATE ; ELIXIR-UK |
PMID:28585923 | Free, Freely available | SCR_019236 | 2026-02-17 10:03:57 | 0 | ||||||||
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BioDepot-workflow-builder Resource Report Resource Website 1+ mentions |
BioDepot-workflow-builder (RRID:SCR_017402) | Bwb | software application, data processing software, software resource, workflow software | Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results. | bioinformatics, big, data, workflow, reproducible, Docker | NIGMS R01 GM126019; NHLBI U54 HL127624; NHGRI U24HG012674; NIAID R03AI159286 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-02-17 10:03:13 | 1 | ||||||||
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celltrackR Resource Report Resource Website 1+ mentions |
celltrackR (RRID:SCR_021021) | software application, data processing software, data analysis software, software resource, software toolkit | Software R package to analyze immune cell migration data. Supports pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration.Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length. | Immune cell migration data, dimensional space, cell analysis, cell migration, cell tracks, cell migration data, displacement, confinement ratio, autocorrelation, turning angle, fractal dimension | is listed by: CRAN | NIAID U01 AI095550; NIAID R01 AI077600 |
DOI:10.1101/670505v1 | Free, Available for download, Freely available | https://github.com/ingewortel/celltrackR | SCR_021021 | 2026-02-17 10:03:42 | 7 | |||||||
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Differential Gene Correlation Analysis Resource Report Resource Website 1+ mentions |
Differential Gene Correlation Analysis (RRID:SCR_020964) | DGCA | data analysis software, software application, data processing software, software resource | Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix. | Differential gene, gene, gene correlation, correlation analysis, input matrices, differential correlations, identifier pairs, gene expression data, calculate differential correlations | is listed by: CRAN | NIA F30 AG052261; NIA R01 AG046170; NCI R01 CA163772; NIAID U01 AI111598 |
PMID:27846853 | Free, Available for download, Freely available | https://github.com/andymckenzie/DGCA | SCR_020964 | 2026-02-17 10:03:55 | 1 | ||||||
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | image processing software, software application, data processing software, software resource | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; NIAID R01AI130303; NSF NSF-1707316; NIMH R01MH110932; NIGMS F31GM116517; NINDS R01NS095367; NIMH P50MH09427; NIH Office of the Director DP2OD006514; NINDS R01NS076467; NINDS U01NS090449; NIGMS P41GM10371; Multidisciplinary University Research Initiative Army Research Office |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-02-17 10:04:29 | 0 | ||||||||
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EASE: the Expression Analysis Systematic Explorer Resource Report Resource Website 50+ mentions |
EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) | EASE | software application, data processing software, software resource | Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible | gene, microarray, genome, gene ontology, statistical analysis, enrichment analysis, FASEB list |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Database for Annotation Visualization and Integrated Discovery |
NIAID | PMID:12734009 PMID:19131956 PMID:19033363 |
Free for academic use | nlx_149218 | SCR_013361 | Expression Analysis Systematic Explorer | 2026-02-17 10:02:23 | 94 | |||||
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ImmuneSpace Resource Report Resource Website 10+ mentions |
ImmuneSpace (RRID:SCR_010508) | data or information resource, portal, organization portal | A consortium of university groups to characterize human immune populations. The Human Immunology Project Consortium (HIPC) program, established in 2010 by the NIAID Division of Allergy, Immunology, and Transplantation, is a major collaborative effort that is generating large amounts of cross-center and cross-assay data including high-dimensional data to characterize the status of the immune system in diverse populations under both normal conditions and in response to stimuli. This large data problem has given birth to ImmuneSpace, a powerful data management and analysis engine where datasets can be easily explored and analyzed using state-of-the-art computational tools. | immunology | has parent organization: Human Immunology Project Consortium | NIAID | nlx_158717 | SCR_010508 | immune space, Immunespace.org | 2026-02-17 10:01:30 | 12 | ||||||||
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NS-Forest Resource Report Resource Website 1+ mentions |
NS-Forest (RRID:SCR_018348) | software application, data processing software, software resource | Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy. | Single cell, RNAseq experiment, generated gene list, minimum set, marker gene, define cell type cluster, random forest, decision tree, machine learning, identify cell, cell clasyfication | is related to: Allen Institute for Brain Science | Allen Institute for Brain Science ; JCVI Innovation Fund ; NIAID R21 AI122100; NIAID U19 AI118626; California Institute for Regenerative Medicine ; Wellcome Trust ; Chan Zuckerberg Initiative DAF |
PMID:29590361 | Free, Available for download, Freely available | SCR_018348 | Necessary and Sufficient Forest, NS-Forestversion 1.3, NS-Forest v2.0, NS-Forest version 1.0 | 2026-02-17 10:03:27 | 2 | |||||||
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proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | data analysis software, software application, data processing software, software resource | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIA R01 AG046170; NIAID U19 AI118610 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-02-17 10:03:11 | 1 | |||||||
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MUMmer Resource Report Resource Website 100+ mentions |
MUMmer (RRID:SCR_018171) | software application, data processing software, software resource, image analysis software, alignment software | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NLM R01 LM06845; NSF IIS 9902923; NIAID N01 AI15447 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer https://bio.tools/mummer https://sources.debian.org/src/mummer/ |
SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-02-17 10:03:43 | 480 |
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