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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-08-01 12:04:32 | 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 | 2026-08-01 12:04:32 | 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 | 2026-08-01 12:04:29 | 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 | 2026-08-01 12:04:33 | 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 | 2026-08-01 12:04:34 | 25 | ||||||||
|
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 | 2026-08-01 12:04:29 | 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 | 2026-08-01 12:04:33 | 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 | 2026-08-01 12:04:29 | 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 | 2026-08-01 12:04:34 | 6 | |||||||||
|
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 | 2026-08-01 12:04:28 | 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 | 2026-08-01 12:04:28 | 29 | |||||
|
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 | 2026-08-01 12:04:33 | 56 | |||||||
|
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 | 2026-08-01 12:04:33 | 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 | 2026-08-01 12:04:34 | 0 | |||||||
|
VirVarSeq Resource Report Resource Website 10+ mentions |
VirVarSeq (RRID:SCR_012116) | software resource | Software for a low frequency Virus Variant detection pipeline for Illumina data. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25178459 | OMICS_05534 | SCR_012116 | 2026-08-01 12:04:36 | 11 | |||||||||
|
Pegasus-fus Resource Report Resource Website 10+ mentions |
Pegasus-fus (RRID:SCR_012118) | software resource | Software that annotates biologically functional gene fusion candidates. | standalone software, unix/linux, java, perl, python |
is used by: Cumulus is listed by: OMICtools has parent organization: SourceForge |
PMID:25183062 | OMICS_05584 | SCR_012118 | 2026-08-01 12:04:34 | 14 | |||||||||
|
WaveCNV Resource Report Resource Website 1+ mentions |
WaveCNV (RRID:SCR_012244) | WaveCNV | software resource | Cancer specific CNV caller for Next Generation sequence. | cancer | is listed by: OMICtools | PMID:24192544 | OMICS_00353 | SCR_012244 | 2026-08-01 12:04:36 | 2 | ||||||||
|
Burrows-Wheeler transform Resource Report Resource Website 1+ mentions |
Burrows-Wheeler transform (RRID:SCR_012304) | BWT | software resource | Software tool as data transformation algorithm that restructures data in such a way that the transformed message is more compressible. Used for large scale compression of genomic sequence databases. | Large scale compression, data transformation, genomic sequence databases compression, |
is listed by: OMICtools is related to: RopeBWT2 is related to: BEETL-fastq |
PMID:22556365 | Free, Freely available | OMICS_00950 | SCR_012304 | Burrows-Wheeler Transform | 2026-08-01 12:04:35 | 8 | ||||||
|
npstat Resource Report Resource Website 1+ mentions |
npstat (RRID:SCR_012128) | software resource | Software that implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:24102736 | OMICS_05826 | SCR_012128 | 2026-08-01 12:04:34 | 3 | |||||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | Network Analysis and Inference Library | 2026-08-01 12:04:35 | 8 |
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.
