Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Joint Acquisition, Recording and Voxel based Inference System Resource Report Resource Website 1+ mentions |
Joint Acquisition, Recording and Voxel based Inference System (RRID:SCR_022723) | JARVIS | software toolkit, software resource | Software markerless 3D motion capture toolbox. Used for capturing precise 3D motion. | markerless 3D motion capture, capturing precise 3D motion | Free, Available for download, Freely available | https://github.com/JARVIS-MoCap | SCR_022723 | JARVIS-MoCap | 2026-08-09 09:08:26 | 1 | ||||||||
|
zmax_edf_merge_converter Resource Report Resource Website |
zmax_edf_merge_converter (RRID:SCR_022567) | software application, software resource | Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format. | hypnodyne, Zmax, converter, EDF, merge, python, windows | Free, Available for download, Freely available | SCR_022567 | 2026-08-09 09:07:58 | 0 | |||||||||||
|
ordinal Resource Report Resource Website 1+ mentions |
ordinal (RRID:SCR_022856) | software toolkit, software resource | Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models. | ordered categorical data, cumulative link models, ordered regression models, proportional odds models, proportional hazards models, grouped survival times | is listed by: CRAN | Free, Available for download, Freely available | SCR_022856 | Regression Models for Ordinal Data | 2026-08-09 09:08:25 | 9 | |||||||||
|
Coselens Resource Report Resource Website 1+ mentions |
Coselens (RRID:SCR_022578) | software toolkit, software resource | Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups. | detect gene level differential selection, selection between two groups of samples, calculation of excess mutation, non synonymous mutations, | Spanish Ministry of Science | DOI:10.1101/2022.01.10.475617 | Free, Available for download, Freely available | SCR_022578 | COnditional SELection on the Excess of NonSynonymous Substitutions | 2026-08-09 09:08:19 | 3 | ||||||||
|
bio_contrast_subgraph Resource Report Resource Website 1+ mentions |
bio_contrast_subgraph (RRID:SCR_022853) | software toolkit, software resource | Software package for implementing algorithms proposed in Lanciano et al. "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data". | , Comparing Homogeneous and Heterogeneous Networks, Omics Data | Free, Available for download, Freely available | SCR_022853 | 2026-08-09 09:08:28 | 1 | |||||||||||
|
ISGPRE Resource Report Resource Website 1+ mentions |
ISGPRE (RRID:SCR_022730) | software toolkit, software resource | Software package for predicting interferon stimulated human genes. | predicting interferon stimulated human genes, interferon stimulated human genes, human genes | DOI:10.1101/2021.10.08.463622 | Free, Available for download, Freely available | http://isgpre.cvr.gla.ac.uk/ | SCR_022730 | 2026-08-09 09:08:03 | 1 | |||||||||
|
EnrichedHeatmap Resource Report Resource Website 50+ mentions |
EnrichedHeatmap (RRID:SCR_023082) | software toolkit, software resource | Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites. | visualization of genomic signal associations, enrichment of genomic signals, specific target regions, | German Cancer Research Center-Heidelberg Center for Personalized Oncology | PMID:29618320 | Free, Available for download, Freely available | https://bioconductor.org/packages/EnrichedHeatmap/ | SCR_023082 | 2026-08-09 09:08:12 | 78 | ||||||||
|
SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software toolkit, software resource | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950; NCI U24CA143835; American Cancer Society Research Scholar Grant |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SYstems Genetic Network AnaLysis | 2026-08-09 09:08:30 | 1 | ||||||||
|
Algorithms and Framework for Nonnegative Matrix Factorization Resource Report Resource Website 10+ mentions |
Algorithms and Framework for Nonnegative Matrix Factorization (RRID:SCR_023124) | NMF | software toolkit, software resource | Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. | Non-negative Matrix Factorization, nonnegative matrix factorization, |
is listed by: CRAN is related to: NMF Toolbox |
South-African National Bioinformatics Network ; Science Foundation Ireland |
DOI:10.1186/1471-2105-11-367 | Free, Available for download, Freely available | SCR_023124 | Non-negative Matrix Factorization | 2026-08-09 09:08:13 | 13 | ||||||
|
Automated Fiber Quantification in Python Resource Report Resource Website 10+ mentions |
Automated Fiber Quantification in Python (RRID:SCR_023366) | pyAFQ | software toolkit, software resource | Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry. | Automates tractometry, automated delineation of major fiber tracts, individual human brains, quantification of tissue properties, tissue properties within fiber tracts, diffusion MRI data, | NIMH 1RF1MH121868; The BRAIN Initiative ; Gordon and Betty Moore Foundation ; Alfred P. Sloan Foundation ; NIBIB R01EB027585; NSF 1551330 |
PMID:35079748 | Free, Available for download, Freely available | SCR_023366 | 2026-08-09 09:08:36 | 12 | ||||||||
|
SigProfilerMatrixGenerator Resource Report Resource Website 10+ mentions |
SigProfilerMatrixGenerator (RRID:SCR_023122) | software application, software resource | Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions. | mutational patterns, small mutational events, create mutational matrices, somatic mutations, samples with associated mutational catalogues, | is related to: SigProfilerExtractor | Cancer Research UK Grand Challenge Award ; Singapore Ministry of Health ; Singapore National Medical Research Council |
PMID:31470794 | Free, Available for download, Freely available | https://osf.io/s93d5/wiki/home | SCR_023122 | 2026-08-09 09:08:31 | 35 | |||||||
|
Regression Modeling Strategies Resource Report Resource Website 10+ mentions |
Regression Modeling Strategies (RRID:SCR_023242) | rms | software toolkit, software resource | Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression. | streamline modeling, regression models, regression, generalized linear models | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/harrelfe/rms, https://cran.r-project.org/web/packages/rms/rms.pdf | SCR_023242 | 2026-08-09 09:08:33 | 41 | ||||||||
|
MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software toolkit, software resource | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NSF DEB-2028280; NIAID U19AI110820; NHGRI R01HG005220; NIDDK R24DK110499; NIDDK U54DK102557 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-08-09 09:08:34 | 212 | ||||||||
|
FFTrees Resource Report Resource Website |
FFTrees (RRID:SCR_023359) | software toolkit, software resource | Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate. | decision algorithm, solving binary classification problems, binary classification, | is listed by: CRAN | DOI:10.1017/S1930297500006239 | Free, Available for download, Freely available | https://CRAN.R-project.org/package=FFTrees | SCR_023359 | Fast-and-Frugal Trees | 2026-08-09 09:08:35 | 0 | |||||||
|
ReMM score Resource Report Resource Website 1+ mentions |
ReMM score (RRID:SCR_023095) | ReMM score | software application, software resource | Software tool that scores positions in human genome in terms of their regulatory probability. Regulatory Mendelian Mutation score was created for relevance prediction of non-coding variations (SNVs and small InDels) in human genome (hg19) in terms of Mendelian diseases. | positions in human genome scoring, regulatory probability, relevance prediction, non-coding variations, SNVs and small InDels, Mendelian diseases, human genome | DOI:10.1101/2022.03.14.484240 | Free, Available for download, Freely available | https://charite.github.io/software-remm-score.html, https://search.datacite.org/works/10.5281/zenodo.1197579 | SCR_023095 | Regulatory Mendelian Mutation score | 2026-08-09 09:08:30 | 6 | |||||||
|
EnTAP Resource Report Resource Website 10+ mentions |
EnTAP (RRID:SCR_023010) | software toolkit, software resource | Software package as eukaryotic non model annotation pipeline.Used for bringing functional annotation to non-model eukaryotic transcriptomes to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. Addresses fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts. | functional annotation, non model eukaryotic transcriptomes, functional gene annotation, de novo assembled transcriptomes, non-model eukaryotes, protein-coding transcripts, | has parent organization: University of Connecticut; Connecticut; USA | DOI:10.1111/1755-0998.13106 | Free, Available for download, Freely available | SCR_023010 | Eukaryotic Non-Model Transcriptome Annotation Pipeline | 2026-08-09 09:08:30 | 20 | ||||||||
|
ATACseqQC Resource Report Resource Website 50+ mentions |
ATACseqQC (RRID:SCR_023103) | software toolkit, software resource | Software R package for post alignment quality assessment of ATAC-seq data. Package also contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. | Assays for Transposase-Accessible Chromatin, sequencing, quality control, assaying chromatin accessibility, post alignment quality assessment, ATAC-seq data, preprocess aligned ATAC-seq data, subsequent peak calling, | Department of Molecular ; Cell and Cancer Biology at UMass Medical School |
PMID:29490630 | Free, Available for download, Freely available | SCR_023103 | Assays for Transposase-Accessible Chromatin using sequencing Quality Control | 2026-08-09 09:08:31 | 60 | ||||||||
|
ENCODE ATAC-seq pipeline Resource Report Resource Website 100+ mentions |
ENCODE ATAC-seq pipeline (RRID:SCR_023100) | software toolkit, software resource | Software pipeline to process ATAC-Seq data. Used for automated end-to-end quality control and processing of ATAC-seq and DNase-seq data. | automated end-to-end quality control and processing, ATAC-seq, DNase-seq data, | Free, Available for download, Freely available | SCR_023100 | 2026-08-09 09:08:13 | 155 | |||||||||||
|
10x Genomics Cellranger DNA Resource Report Resource Website 50+ mentions |
10x Genomics Cellranger DNA (RRID:SCR_023221) | software toolkit, software resource | Software analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation, and compare heterogeneity among cells. Used in processing of single cell DNA sequencing performed on 10x Chromium platform. | 10x Chromium platform, single cell DNA sequencing processing, Chromium single cell DNA sequencing, align reads, identify copy number variation, compare heterogeneity among cells, | Restricted | SCR_023221 | Cell Ranger DNA, 10x Genomics Cellranger DNA software, 10x Genomics Cellranger software | 2026-08-09 09:08:14 | 92 | ||||||||||
|
vtree Resource Report Resource Website 1+ mentions |
vtree (RRID:SCR_023458) | software toolkit, software resource | Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame. | Display information, nested subsets, data frame, calculating and drawing variable trees, variable trees | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/nbarrowman/vtree | SCR_023458 | variable tree | 2026-08-09 09:08:16 | 1 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
