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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CCAT (Combinatorial Code Analysis Tool) Resource Report Resource Website |
CCAT (Combinatorial Code Analysis Tool) (RRID:SCR_012028) | CCAT (Combinatorial Code Analysis Tool) | software resource | A software package for predicting genome-wide co-binding between biological regulators such as Transcription factors (TFs). | windows |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
PMID:24366875 | Apache License | OMICS_02179 | SCR_012028 | 2026-08-08 11:59:56 | 0 | |||||||
|
digitagCT Resource Report Resource Website 1+ mentions |
digitagCT (RRID:SCR_012027) | digitagCT | software resource | Software that combines digital gene expression (DGE) tags, RNA-Seq, tiling array expression data and species-comparison to explore new transcriptional regions and their specific biological features, particularly tissue expression or conservation. | digital gene expression, rna-seq |
is listed by: OMICtools has parent organization: National Institute for Research in Computer Science and Control; Brittany; France |
PMID:24357408 | OMICS_02178 | SCR_012027 | 2026-08-08 11:59:38 | 1 | ||||||||
|
AnalyzeReplication Resource Report Resource Website |
AnalyzeReplication (RRID:SCR_012030) | AnalyzeReplication | software resource | Source code providing a cost-effectiveness metric for guiding the design of large-scale RNA-seq differentially expressed (DE) studies. | rna-seq, differential expression |
is listed by: OMICtools is related to: Gene Expression Omnibus has parent organization: University of Chicago; Illinois; USA |
PMID:24319002 | Free, Public | OMICS_02194 | SCR_012030 | 2026-08-08 11:59:38 | 0 | |||||||
|
Scramble Resource Report Resource Website 10+ mentions |
Scramble (RRID:SCR_012036) | software resource | A C software implementation of SAM, BAM and CRAM file I/O. | standalone software, c, c++, fortran |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24930138 | BSD License | OMICS_04662 | SCR_012036 | 2026-08-08 11:59:56 | 21 | ||||||||
|
CowCoDA Resource Report Resource Website |
CowCoDA (RRID:SCR_012039) | software resource | Software that performs retention time alignment on the given set of peaks. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18715018 | OMICS_02380 | SCR_012039 | 2026-08-08 12:00:05 | 0 | |||||||||
|
OBI-Warp Resource Report Resource Website 1+ mentions |
OBI-Warp (RRID:SCR_012041) | software resource | Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:16944896 | MIT License | OMICS_02386, biotools:obi-warp | https://bio.tools/obi-warp | SCR_012041 | Ordered Bijective Interpolated Warping | 2026-08-08 11:59:56 | 2 | ||||||
|
TOPP Resource Report Resource Website 10+ mentions |
TOPP (RRID:SCR_012044) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17237091 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02451 | SCR_012044 | 2026-08-08 11:59:56 | 25 | ||||||||
|
CPFP Resource Report Resource Website 1+ mentions |
CPFP (RRID:SCR_012043) | software resource, software application, data analysis software, data processing software | Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:20189941 | OMICS_02448, biotools:cpfp | https://bio.tools/cpfp | SCR_012043 | Central Proteomics Facilities Pipeline | 2026-08-08 11:59:39 | 7 | |||||||
|
Antilope Resource Report Resource Website 1+ mentions |
Antilope (RRID:SCR_012046) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21464512 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02481 | SCR_012046 | 2026-08-08 11:59:39 | 4 | ||||||||
|
swissPIT Resource Report Resource Website |
swissPIT (RRID:SCR_012045) | software resource | Software for pipelined analysis of mass spectrometry data. |
is listed by: OMICtools has parent organization: SourceForge has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:18436540 | GNU General Public License | OMICS_02452 | SCR_012045 | Swiss Protein Identification Toolbox | 2026-08-08 12:00:05 | 0 | ||||||||
|
ICPL ESIQuant Resource Report Resource Website |
ICPL ESIQuant (RRID:SCR_012047) | software resource | A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23454610 | biotools:icpl_esiquant, OMICS_02490 | https://bio.tools/icpl_esiquant | SCR_012047 | 2026-08-08 11:59:56 | 0 | ||||||||
|
COALESCE Resource Report Resource Website 1+ mentions |
COALESCE (RRID:SCR_012005) | COALESCE | software resource | Software that can use large collections of genomic data and Bayesian integration to predict coregulated gene modules, the conditions of regulation, and the consensus binding motifs for regulation. | is listed by: OMICtools | OMICS_01804 | SCR_012005 | Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction | 2026-08-08 12:00:04 | 6 | |||||||||
|
Bioinformatics Organization Resource Report Resource Website 100+ mentions |
Bioinformatics Organization (RRID:SCR_012008) | Bioinformatics.Org | data or information resource, short course, production service resource, software resource, data analysis service, training resource, community building portal, data set, analysis service resource, service resource, portal, job resource | Organization that serves the scientific and educational needs of bioinformatic practitioners and the general public. They develop and maintain computational resources to facilitate world-wide communications and collaborations between people of all educational and professional levels. They provide and promote open access to the materials and methods required for, and derived from, research, development and education. | bioinformatics |
is listed by: OMICtools is parent organization of: BioWiki |
The community can contribute to this resource | OMICS_01825 | SCR_012008 | 2026-08-08 11:59:56 | 298 | ||||||||
|
Bionotate Resource Report Resource Website 1+ mentions |
Bionotate (RRID:SCR_012098) | production service resource, software resource, data analysis service, analysis service resource, service resource | An open source annotation tool for the distributed creation of a large corpus. | web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19232400 | GNU General Public License | OMICS_05229 | SCR_012098 | 2026-08-08 12:00:07 | 1 | ||||||||
|
Genome Alteration Print Resource Report Resource Website 1+ mentions |
Genome Alteration Print (RRID:SCR_012016) | GAP | software resource | Software for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes. | genome, segmental copy number, genotype, genome profile, copy number, single-nucleotide polymorphism, array |
is listed by: OMICtools has parent organization: Curie Institute; Paris; France |
Cancer, Tumor | PMID:19903341 | OMICS_02119 | SCR_012016 | Genome Alteration Print (GAP): Mining complex cancer genomic profiles | 2026-08-08 11:59:56 | 4 | ||||||
|
easyRNASeq Resource Report Resource Website 10+ mentions |
easyRNASeq (RRID:SCR_012020) | easyRNASeq | software resource | Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package. | rna-seq, gene expression, genetics, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Molecular Biology Laboratory |
PMID:22847932 | Artistic License, v2 | OMICS_01938, biotools:easyrnaseq | https://bio.tools/easyrnaseq | SCR_012020 | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-08-08 11:59:38 | 30 | |||||
|
VisSR Resource Report Resource Website 1+ mentions |
VisSR (RRID:SCR_012024) | VisSR | software resource, software application, data visualization software, data processing software | Software to generate a visual representation of sRNAs and user-imported genomic features. The tool may be run on its own or from other tools, e.g. miRCat. |
is listed by: OMICtools is listed by: UEA sRNA Workbench is listed by: bio.tools is listed by: Debian has parent organization: University of East Anglia; Norwich; United Kingdom |
OMICS_02107, biotools:vissr | https://bio.tools/vissr | SCR_012024 | Visualisation of sRNAs | 2026-08-08 11:59:38 | 3 | ||||||||
|
MToolBox Resource Report Resource Website 50+ mentions |
MToolBox (RRID:SCR_012112) | software resource | Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25028726 | GNU General Public License | OMICS_05466, biotools:mtoolbox | https://bio.tools/mtoolbox | SCR_012112 | 2026-08-08 11:59:57 | 57 | |||||||
|
Allim Resource Report Resource Website 1+ mentions |
Allim (RRID:SCR_012114) | software resource | A user-friendly software tool to estimate allele-specific gene expression. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:23615333 | biotools:allim, OMICS_05504 | https://bio.tools/allim | SCR_012114 | 2026-08-08 11:59:40 | 2 | ||||||||
|
ReviSTER Resource Report Resource Website |
ReviSTER (RRID:SCR_012113) | software resource | Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23677944 | GNU General Public License | OMICS_05468 | SCR_012113 | Revise Simple Tandem repeat Error Reads | 2026-08-08 12:00:07 | 0 |
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.
