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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BRAINSTracer Resource Report Resource Website 1+ mentions |
BRAINSTracer (RRID:SCR_012894) | BRAINSTracer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155705 | http://www.nitrc.org/projects/brainstracer | SCR_012894 | 2026-08-01 12:04:42 | 5 | |||||||
|
National Science Foundation Resource Report Resource Website 1000+ mentions |
National Science Foundation (RRID:SCR_012938) | NSF | institution | An independent federal agency created by Congress to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense They are the funding source for approximately 20 percent of all federally supported basic research conducted by America''s colleges and universities. In many fields such as mathematics, computer science and the social sciences, NSF is the major source of federal backing. NSF leadership has two major components: a director who oversees NSF staff and management responsible for program creation and administration, merit review, planning, budget and day-to-day operations; and a 24-member National Science Board (NSB) of eminent individuals that meets six times a year to establish the overall policies of the foundation.The director and all Board members serve six year terms. Each of them, as well as the NSF deputy director, is appointed by the President of the United States and confirmed by the U.S. Senate. At present, NSF has a total workforce of about 2,100 at its Arlington, Va., headquarters, including approximately 1,400 career employees, 200 scientists from research institutions on temporary duty, 450 contract workers and the staff of the NSB office and the Office of the Inspector General. NSF is the only federal agency whose mission includes support for all fields of fundamental science and engineering, except for medical sciences. They are tasked with keeping the United States at the leading edge of discovery in areas from astronomy to geology to zoology. So, in addition to funding research in the traditional academic areas, the agency also supports high-risk, high pay-off ideas, novel collaborations and numerous projects that may seem like science fiction today, but which the public will take for granted tomorrow. And in every case, they ensure that research is fully integrated with education so that today''s revolutionary work will also be training tomorrow''s top scientists and engineers NSF''s task of identifying and funding work at the frontiers of science and engineering is not a top-down process. |
is related to: DMPTool is parent organization of: NSDL: The National Science Digital Library is parent organization of: CIPRES Science Gateway is parent organization of: dCAPS Finder is parent organization of: Scholarpedia is parent organization of: Chlamydomonas Resource Center is parent organization of: Bacillus Genetic Stock Center (BGSC) is parent organization of: Sheep Brain Atlas is parent organization of: Advanced Cyberinfrastructure Coordination Ecosystem Services and Support Core Facility |
grid.431093.c, Wikidata: Q304878, ISNI: 0000 0001 1958 7073, Crossref funder ID: 100000001, nlx_inv_1005118 | https://ror.org/021nxhr62 | SCR_012938 | National Science Foundation | 2026-08-01 12:04:43 | 2070 | ||||||||
|
DNaseR Resource Report Resource Website |
DNaseR (RRID:SCR_012819) | DNaseR | software resource | A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23118738 | Free | biotools:dnaser, OMICS_00517 | https://bio.tools/dnaser | SCR_012819 | DNaseR: DNase I footprinting analysis of DNase-seq data | 2026-08-01 12:04:40 | 0 | |||||
|
Acacia Resource Report Resource Website 100+ mentions |
Acacia (RRID:SCR_012896) | Acacia | software resource | Accurate error-correction of amplicon pyrosequences. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
DOI:10.1038/nmeth.1990 | OMICS_01116 | https://sources.debian.org/src/acacia/ | SCR_012896 | 2026-08-01 12:04:53 | 106 | ||||||||
|
TargetScore Resource Report Resource Website 1+ mentions |
TargetScore (RRID:SCR_012933) | TargetScore | software resource | Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24135265 | Free | OMICS_00421 | SCR_012933 | TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information | 2026-08-01 12:04:53 | 3 | |||||||
|
OncoSNP Resource Report Resource Website 10+ mentions |
OncoSNP (RRID:SCR_012985) | OncoSNP | software resource | An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data. | is listed by: OMICtools | Cancer | Freely available for academic use, Non-commercial, Commercial with permission | OMICS_00728 | SCR_012985 | 2026-08-01 12:04:54 | 19 | ||||||||
|
RLMM Resource Report Resource Website 1+ mentions |
RLMM (RRID:SCR_012984) | RLMM | software resource | A Genotype Calling Algorithm for Affymetrix SNP Arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00732 | SCR_012984 | 2026-08-01 12:04:44 | 5 | ||||||||||
|
IBDLD Resource Report Resource Website 10+ mentions |
IBDLD (RRID:SCR_013043) | IBDLD | software resource | A C++ software program for multipoint IBD estimation based on high density SNP genotype data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21769932 | Free | OMICS_00204 | SCR_013043 | 2026-08-01 12:04:55 | 14 | |||||||
|
SolSNP Resource Report Resource Website 1+ mentions |
SolSNP (RRID:SCR_013045) | SolSNP | software resource | A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. |
is listed by: OMICtools has parent organization: SourceForge |
MIT License | OMICS_00079 | SCR_013045 | 2026-08-01 12:04:55 | 7 | |||||||||
|
HATS Resource Report Resource Website 10+ mentions |
HATS (RRID:SCR_013044) | HATS | software resource | A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00200 | SCR_013044 | Haplotype Amplification in Tumor Sequences | 2026-08-01 12:04:45 | 37 | |||||||||
|
charm Resource Report Resource Website 50+ mentions |
charm (RRID:SCR_012992) | charm | software resource | Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:charm, OMICS_00792 | https://bio.tools/charm | SCR_012992 | 2026-08-01 12:04:43 | 63 | ||||||||
|
ChIPOTle Peak Finder Resource Report Resource Website |
ChIPOTle Peak Finder (RRID:SCR_012991) | ChIPOTle Peak Finder | software resource | A peak-finding algorithm used to analyze ChIP-chip microarray data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00803 | SCR_012991 | 2026-08-01 12:04:54 | 0 | ||||||||||
|
BiSeq Resource Report Resource Website 10+ mentions |
BiSeq (RRID:SCR_012993) | BiSeq | software resource | Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00620 | SCR_012993 | 2026-08-01 12:04:44 | 30 | ||||||||||
|
Trinity Resource Report Resource Website 5000+ mentions |
Trinity (RRID:SCR_013048) | Trinity | software resource | Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Broad Institute has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
DOI:10.1038/nbt.1883 | biotools:trinity, OMICS_01327 | https://bio.tools/trinity, https://sources.debian.org/src/trinityrnaseq/ | SCR_013048 | 2026-08-01 12:04:55 | 9576 | |||||||
|
NGSpeAnalysis Resource Report Resource Website |
NGSpeAnalysis (RRID:SCR_013040) | NGSpeAnalysis | software resource | A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00291 | SCR_013040 | 2026-08-01 12:04:44 | 0 | |||||||||
|
MEDME Resource Report Resource Website 10+ mentions |
MEDME (RRID:SCR_012995) | MEDME | software resource | Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00614 | SCR_012995 | 2026-08-01 12:04:54 | 18 | ||||||||||
|
MethylCoder Resource Report Resource Website 1+ mentions |
MethylCoder (RRID:SCR_012997) | MethylCoder | software resource | A single program that takes of bisulfite-treated reads and outputs per-base methylation data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21724594 | biotools:methylcoder, OMICS_00585 | https://bio.tools/methylcoder | SCR_012997 | 2026-08-01 12:04:44 | 4 | |||||||
|
LoFreq Resource Report Resource Website 500+ mentions |
LoFreq (RRID:SCR_013054) | LoFreq | software resource | A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23066108 DOI:10.1093/nar/gks918 |
Free, Freely available | OMICS_00063 | https://sources.debian.org/src/lofreq/ | SCR_013054 | LoFreq - Sensitive variant-calling from sequencing data | 2026-08-01 12:04:55 | 523 | ||||||
|
GENE-counter Resource Report Resource Website 1+ mentions |
GENE-counter (RRID:SCR_013056) | GENE-counter | software resource | A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21998647 | OMICS_01404, biotools:gene-counter | https://bio.tools/gene-counter | SCR_013056 | 2026-08-01 12:04:44 | 7 | |||||||
|
RNA CoMPASS Resource Report Resource Website |
RNA CoMPASS (RRID:SCR_013058) | RNA CoMPASS | software resource | A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01410 | SCR_013058 | 2026-08-01 12:04:55 | 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.
