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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ISDTool Resource Report Resource Website |
ISDTool (RRID:SCR_012125) | software resource | Software that implements a computational model for predicting immunosuppressive domains (ISDs). The software could be used to identify typical ISDs in retroviruses including HERV, HTLV, HIV, STLV, SIV and MLV. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25008418 | OMICS_05696, biotools:isdtool | https://bio.tools/isdtool | SCR_012125 | 2026-08-01 12:04:36 | 0 | ||||||||
|
A5-miseq Resource Report Resource Website 100+ mentions |
A5-miseq (RRID:SCR_012148) | software resource | Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming. | standalone software, illumina, unix/linux, mac os x, bio.tools |
is used by: Nephele is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25338718 | GNU General Public License | OMICS_06339, biotools:a5-miseq | https://bio.tools/a5-miseq | SCR_012148 | 2026-08-01 12:04:34 | 189 | |||||||
|
EC2KEGG Resource Report Resource Website 1+ mentions |
EC2KEGG (RRID:SCR_012127) | software resource | A perl-based package to perform comparative analysis of metabolic pathways between two organisms. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25202338 | OMICS_05782 | SCR_012127 | 2026-08-01 12:04:34 | 8 | |||||||||
|
cnvCapSeq Resource Report Resource Website 1+ mentions |
cnvCapSeq (RRID:SCR_012126) | software resource | Software for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25228465 | GNU Lesser General Public License | OMICS_05722 | SCR_012126 | 2026-08-01 12:04:34 | 2 | ||||||||
|
eALPS Resource Report Resource Website |
eALPS (RRID:SCR_012130) | software resource | Software that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD). | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24144111 | OMICS_05833 | SCR_012130 | 2026-08-01 12:04:36 | 0 | |||||||||
|
PLEK Resource Report Resource Website 100+ mentions |
PLEK (RRID:SCR_012132) | software resource | An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data. | standalone software, roche, pacific biosciences, unix/linux, c, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25239089 | GNU General Public License | biotools:plek, OMICS_05839 | https://bio.tools/plek | SCR_012132 | PLEK: predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme | 2026-08-01 12:04:34 | 122 | ||||||
|
LDx Resource Report Resource Website |
LDx (RRID:SCR_012131) | software resource | A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23152785 | OMICS_05834 | SCR_012131 | 2026-08-01 12:04:34 | 0 | |||||||||
|
REDItools Resource Report Resource Website 100+ mentions |
REDItools (RRID:SCR_012133) | software resource | A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data. | standalone software, illumina, roche, pacific biosciences, life technologies, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:23742983 | MIT License | biotools:reditools, OMICS_05860 | https://bio.tools/reditools | SCR_012133 | 2026-08-01 12:04:35 | 141 | |||||||
|
PrimerProspector Resource Report Resource Website 10+ mentions |
PrimerProspector (RRID:SCR_012136) | software resource | A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21349862 | OMICS_05884 | SCR_012136 | 2026-08-01 12:04:34 | 25 | |||||||||
|
iceLogo Resource Report Resource Website 100+ mentions |
iceLogo (RRID:SCR_012137) | software resource | Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol. | standalone software, web app, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:19876014 | Apache License | biotools:icelogo, OMICS_05885 | https://bio.tools/icelogo | SCR_012137 | 2026-08-01 12:04:35 | 176 | |||||||
|
Musite Resource Report Resource Website 10+ mentions |
Musite (RRID:SCR_012141) | software resource | A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20702892 | OMICS_05941 | SCR_012141 | 2026-08-01 12:04:35 | 12 | |||||||||
|
AMS Resource Report Resource Website |
AMS (RRID:SCR_012140) | software resource | Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22555647 | Apache License | OMICS_05934, biotools:ams | https://bio.tools/ams | SCR_012140 | AutoMotif Service | 2026-08-01 12:04:34 | 0 | ||||||
|
PhosphoSiteAnalyzer Resource Report Resource Website |
PhosphoSiteAnalyzer (RRID:SCR_012142) | software resource | A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22471441 | Free, Public | biotools:phosphositeanalyzer, OMICS_05951 | https://bio.tools/phosphositeanalyzer | SCR_012142 | 2026-08-01 12:04:36 | 0 | |||||||
|
HLAforest Resource Report Resource Website 1+ mentions |
HLAforest (RRID:SCR_012146) | software resource | Software that predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bow tie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest. | standalone software, perl |
is listed by: OMICtools has parent organization: Google Code |
PMID:23840783 | Free for academic use, Apache License | OMICS_06170 | SCR_012146 | 2026-08-01 12:04:35 | 6 | ||||||||
|
DNAcopy Resource Report Resource Website 100+ mentions |
DNAcopy (RRID:SCR_012560) | DNAcopy | software resource | Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
OMICS_00720, biotools:dnacopy | https://bio.tools/dnacopy, https://sources.debian.org/src/r-bioc-dnacopy/ | SCR_012560 | 2026-08-01 12:04:46 | 334 | ||||||||
|
ExiMiR Resource Report Resource Website 1+ mentions |
ExiMiR (RRID:SCR_012753) | ExiMiR | software resource | R functions for the normalization of Exiqon miRNA array data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00783 | SCR_012753 | 2026-08-01 12:04:51 | 1 | ||||||||||
|
CNV Workshop Resource Report Resource Website 1+ mentions |
CNV Workshop (RRID:SCR_012635) | CNV Workshop | software resource | Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV). |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00715 | SCR_012635 | 2026-08-01 12:04:48 | 1 | |||||||||
|
motifRG Resource Report Resource Website 1+ mentions |
motifRG (RRID:SCR_012602) | motifRG | software resource | Software tools for discriminative motif discovery using regression methods. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24162561 | Free | OMICS_00487 | SCR_012602 | motifRG - A package for discriminative motif discovery designed for high throughput sequencing dataset | 2026-08-01 12:04:38 | 5 | |||||||
|
MiRaGE Resource Report Resource Website 10+ mentions |
MiRaGE (RRID:SCR_012738) | MiRaGE | software resource | Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00785 | SCR_012738 | 2026-08-01 12:04:40 | 29 | ||||||||||
|
CexoR Resource Report Resource Website |
CexoR (RRID:SCR_012769) | CexoR | software resource | Software for strand specific peak-pair calling in ChIP-exo replicates. |
is listed by: OMICtools has parent organization: Bioconductor |
MIT License | OMICS_00519 | SCR_012769 | CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates | 2026-08-01 12:04:39 | 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.
