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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
RAMMCAP Resource Report Resource Website 1+ mentions |
RAMMCAP (RRID:SCR_011927) | RAMMCAP | software resource | Metagenomic software pipeline for analysis and comparison of very large metagenomes with fast clustering and functional annotation. | metagenomic |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:19863816 | OMICS_01481 | SCR_011927 | Rapid analysis of Multiple Metagenomes with Clustering and Annotation Pipeline | 2026-08-08 12:00:02 | 2 | |||||||
|
GenomeCloud Resource Report Resource Website |
GenomeCloud (RRID:SCR_011886) | GenomeCloud | storage service resource, data repository, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data | genome | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01219 | SCR_011886 | 2026-08-08 11:59:54 | 0 | ||||||||
|
Scotty Resource Report Resource Website 1+ mentions |
Scotty (RRID:SCR_011889) | Scotty | software resource | A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims. | is listed by: OMICtools | OMICS_01315 | SCR_011889 | Scotty - Power Analysis for RNA Seq Experiments | 2026-08-08 11:59:54 | 9 | |||||||||
|
IsoInfer Resource Report Resource Website |
IsoInfer (RRID:SCR_011892) | IsoInfer | software resource | A C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information. |
is listed by: OMICtools has parent organization: University of California at Riverside; California; USA |
OMICS_01319 | SCR_011892 | 2026-08-08 11:59:55 | 0 | ||||||||||
|
KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | software resource, software application, data analysis software, data processing software | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | 2026-08-08 12:00:01 | 21 | ||||||
|
FusionFinder Resource Report Resource Website 1+ mentions |
FusionFinder (RRID:SCR_011894) | FusionFinder | software resource | A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data. | is listed by: OMICtools | OMICS_01349 | SCR_011894 | FusionHunter: identifying fusion transcripts using paired-end RNA-seq | 2026-08-08 11:59:37 | 4 | |||||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | sequence analysis software, software resource, software application, algorithm resource, data analysis software, data processing software | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-08-08 11:59:36 | 312 | |||||
|
CaMPDB Resource Report Resource Website 1+ mentions |
CaMPDB (RRID:SCR_011976) | CaMPDB | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | Calpain cleavage prediction using multiple kernel learning. | is listed by: OMICtools | PMID:21559271 | OMICS_01669 | SCR_011976 | Calpain for Modulatory Proteolysis Database | 2026-08-08 11:59:38 | 7 | ||||||||
|
NGS Leaders Resource Report Resource Website |
NGS Leaders (RRID:SCR_011982) | NGS Leaders | data or information resource, portal, community building portal | A community created to advance the use and value of next-generation sequencing through knowledge sharing. | is listed by: OMICtools | OMICS_01707 | SCR_011982 | 2026-08-08 11:59:38 | 0 | ||||||||||
|
Guide Resource Report Resource Website 50+ mentions |
Guide (RRID:SCR_011903) | Guide | software resource | A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01405 | SCR_011903 | Guide: Application for gene expression analysis | 2026-08-08 12:00:02 | 63 | ||||||||
|
Oncofuse Resource Report Resource Website 10+ mentions |
Oncofuse (RRID:SCR_011904) | Oncofuse | software resource | Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1093/bioinformatics/btt445 | OMICS_01406 | https://sources.debian.org/src/oncofuse/ | SCR_011904 | 2026-08-08 11:59:37 | 15 | ||||||||
|
PRADA Resource Report Resource Website 50+ mentions |
PRADA (RRID:SCR_011906) | PRADA | software resource | A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01408, biotools:prada-rnaseq | https://bio.tools/prada-rnaseq | SCR_011906 | Pipeline for RNA-Sequencing Data Analysis | 2026-08-08 12:00:02 | 51 | |||||||
|
R-SAP Resource Report Resource Website 1+ mentions |
R-SAP (RRID:SCR_011907) | R-SAP | software resource | An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Georgia Institute of Technology; Georgia; USA |
OMICS_01409, biotools:r-sap | https://bio.tools/r-sap | http://www.mcdonaldlab.biology.gatech.edu/r-sap.htm | SCR_011907 | 2026-08-08 11:59:37 | 3 | |||||||
|
RobiNA Resource Report Resource Website 10+ mentions |
RobiNA (RRID:SCR_011908) | RobiNA | software resource | Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure. | analyse Illumina/Solexa-based RNA-Seq data, data quality control, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22684630 | OMICS_01411 | SCR_011908 | 2026-08-08 11:59:55 | 19 | ||||||||
|
RseqFlow Resource Report Resource Website 1+ mentions |
RseqFlow (RRID:SCR_011909) | RseqFlow | software resource | An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. |
is listed by: OMICtools has parent organization: Google Code |
PMID:21795323 | OMICS_01412 | SCR_011909 | RseqFlow - An RNA-Seq analysis pipeline for Quality Control Expression Level Estimation Differentially Expressed Gene | 2026-08-08 12:00:02 | 3 | ||||||||
|
SeqPipe Resource Report Resource Website |
SeqPipe (RRID:SCR_011862) | SeqPipe | software resource | A command line-based pipeline framework for bioinformatics research. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_01135 | SCR_011862 | 2026-08-08 12:00:00 | 0 | ||||||||||
|
SHORE Resource Report Resource Website 100+ mentions |
SHORE (RRID:SCR_011863) | SHORE | software resource | A mapping and analysis pipeline for short read data produced on the Illumina platform. | is listed by: OMICtools | OMICS_01136 | SCR_011863 | 2026-08-08 11:59:36 | 157 | ||||||||||
|
Stack Overflow Resource Report Resource Website 10+ mentions |
Stack Overflow (RRID:SCR_011984) | Stack Overflow | data or information resource, portal, community building portal | A question and answer site for professional and enthusiast programmers. | programmer | is listed by: OMICtools | Free | OMICS_01711 | SCR_011984 | 2026-08-08 12:00:03 | 23 | ||||||||
|
Bioinformaticsweb Resource Report Resource Website |
Bioinformaticsweb (RRID:SCR_011988) | BIW | data or information resource, portal, topical portal | Open Access Bioinformatics resource portal. | bioinformatics | is listed by: OMICtools | Free | OMICS_01729 | SCR_011988 | 2026-08-08 11:59:38 | 0 | ||||||||
|
HTS Mappers Resource Report Resource Website 1+ mentions |
HTS Mappers (RRID:SCR_011991) | HTS Mappers | software repository, data or information resource, software resource, data set | Data set providing an up-to-date compendium of HTS mappers initially provided in the article Tools for mapping high-throughput sequencing data. Please let fill out the provided form if you are a developer and your mapper is not listed or you want to update the data for your mapper. | mapping, high-throughput sequencing, dna, rna, mirna, bisulfite, mapper |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:23060614 | OMICS_01733 | SCR_011991 | 2026-08-08 12:00:03 | 2 |
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.
