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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SNPdryad Resource Report Resource Website 1+ mentions |
SNPdryad (RRID:SCR_006414) | SNPdryad | service resource | Service to predict deleterious non-synonymous human Single Nucleotide Polymorphisms (SNPs) using only orthologous protein sequences. | non-synonymous, single nucleotide polymorphism, ortholog, protein sequence |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:24389653 | OMICS_02198 | SCR_006414 | SNPdryad - Deleterious Non-Synonymous SNP Predictions for Human | 2026-08-01 12:03:11 | 3 | |||||||
|
QCGWAS Resource Report Resource Website 1+ mentions |
QCGWAS (RRID:SCR_006408) | QCGWAS | software resource | Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies. | quality control, genome wide association study, windows, os x, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24395754 | GNU General Public License, v3 or later | OMICS_02203, biotools:qcgwas | https://bio.tools/qcgwas | SCR_006408 | QCGWAS: Quality Control of Genome Wide Association Study results, Quality Control of Genome Wide Association Study | 2026-08-01 12:03:09 | 7 | |||||
|
Jalview Resource Report Resource Website 1000+ mentions |
Jalview (RRID:SCR_006459) | Jalview | software resource | A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. | edit, analysis, annotation, multiple sequence alignment, wysiwyg, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Dundee; Scotland; United Kingdom |
BBSRC BBSB16542 | PMID:19151095 DOI:10.1093/bioinformatics/btp033 |
GNU General Public License, v3, Acknowledgement requested | OMICS_00885, biotools:Jalview | https://bio.tools/Jalview, https://sources.debian.org/src/jalview/ | SCR_006459 | 2026-08-01 12:03:10 | 3769 | |||||
|
SRAdb Resource Report Resource Website 10+ mentions |
SRAdb (RRID:SCR_006524) | SRAdb | software resource | Software package to make access to the compilation of metadata from NCBI SRA and tools associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI Sequence Read Archive (SRA) has parent organization: Bioconductor |
PMID:23323543 | Artistic License, v2 | biotools:sradb, OMICS_01032 | https://bio.tools/sradb | SCR_006524 | SRAdb - A compilation of metadata from NCBI SRA and tools | 2026-08-01 12:03:09 | 18 | |||||
|
seq crumbs Resource Report Resource Website 1+ mentions |
seq crumbs (RRID:SCR_006486) | seq_crumbs | software resource | A collection of small sequence processing utilities that are modeled after the Unix command line text processing utilities so every utility tries to perform a specific task and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utilities with Unix pipes to create complex pipelines. | is listed by: OMICtools | Mainly under the, GNU General Public License | OMICS_01075 | SCR_006486 | 2026-08-01 12:03:13 | 9 | |||||||||
|
MethylSeekR Resource Report Resource Website 50+ mentions |
MethylSeekR (RRID:SCR_006513) | MethylSeekR | software resource | A software package for the discovery of regulatory regions from Bis-seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00607 | SCR_006513 | MethylSeekR - Segmentation of Bis-seq data | 2026-08-01 12:03:13 | 54 | ||||||||
|
casper Resource Report Resource Website 100+ mentions |
casper (RRID:SCR_006613) | casper | software resource | Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | biotools:casper, OMICS_01270 | https://bio.tools/casper | SCR_006613 | casper - Characterization of Alternative Splicing based on Paired-End Reads, Characterization of Alternative Splicing based on Paired-End Reads | 2026-08-01 12:03:13 | 149 | ||||||
|
SpliceTrap Resource Report Resource Website 10+ mentions |
SpliceTrap (RRID:SCR_006728) | SpliceTrap | software resource | A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3?/5? splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Cold Spring Harbor Laboratory |
PMID:21896509 | biotools:splicetrap, OMICS_01292 | https://bio.tools/splicetrap | SCR_006728 | 2026-08-01 12:03:18 | 16 | |||||||
|
BEDTools Resource Report Resource Website 10000+ mentions |
BEDTools (RRID:SCR_006646) | BEDTools | software resource | A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line. | genomics, bed, sam, bam, overlap, sequencing, intersect, coverage, gff, vcf, bedgraph, interval, genome arithmetic, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Hydra is related to: pybedtools is required by: SL-quant |
PMID:20110278 DOI:10.1093/bioinformatics/btq033 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01159, biotools:bedtools | https://code.google.com/p/bedtools/, https://bio.tools/bedtools, https://sources.debian.org/src/bedtools/ | SCR_006646 | bedtools - a swiss army knife for genome arithmetic, bedtools: a flexible suite of utilities for comparing genomic features | 2026-08-01 12:03:11 | 10394 | |||||
|
ALEXA-Seq Resource Report Resource Website 1+ mentions |
ALEXA-Seq (RRID:SCR_006700) | ALEXA-Seq | software resource | A method for using massively parallel paired-end transcriptome sequencing for ''alternative expression analysis''. | is listed by: OMICtools | OMICS_01328 | SCR_006700 | 2026-08-01 12:03:18 | 6 | ||||||||||
|
SpliceGrapher Resource Report Resource Website 10+ mentions |
SpliceGrapher (RRID:SCR_006657) | SpliceGrapher | software resource | Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22293517 | OMICS_01266 | SCR_006657 | 2026-08-01 12:03:14 | 22 | |||||||||
|
ChIPXpress Resource Report Resource Website 1+ mentions |
ChIPXpress (RRID:SCR_006653) | ChIPXpress | software resource | A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target. | gene expression, chip-seq, chip-chip, transcription factor, target gene, gene, gene expression profile |
is listed by: OMICtools is related to: Gene Expression Omnibus has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00516 | SCR_006653 | ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles | 2026-08-01 12:03:17 | 2 | |||||||
|
SoftSearch Resource Report Resource Website 1+ mentions |
SoftSearch (RRID:SCR_006683) | SoftSearch | software resource | A sensitive structural variant (SV) detection software tool for Illumina paired-end next-generation sequencing data. It simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity. Soft clips are proxies for split-reads that indicate part of the read maps to the reference genome, but the other part is not localized at the same place (e.g. breakpoint spanning reads). Discordant read-pairs refer to a read and its mate, where the insert size is greater (or less than) the expected distribution of the dataset ? or ? where the mapping orientation of the reads is unexpected (e.g. both on the same strand). SoftSearch looks for areas with soft-clipping in the genome that have discordant read pairs supporting the anomaly. Once areas with both these conditions are identified, the read and mate information is extracted directly from the BAM file containing the discordant reads, obviating the need for time-consuming and error-prone complex alignment strategies. Only a small number of soft-masked bases discordant read-pairs are necessary to identify an SV, which on their own would not be sufficient to make an SV call, thus highlighting SoftSearch?s improved sensitivity. SoftSearch is well suited to be ?plugged in? to most sequence analysis workflows, since it requires standard file inputs, such as a BAM file using almost any aligner and a reference genome FASTA file. Because SoftSearch requires soft-masked bases, the only requirement is that the aligner must have this functionality, which is usually turned on by default by many standard aligners (e.g. BWA, Novoalign, etc). | illumina, structural variant, next-generation sequencing, perl, academic |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_00322 | SCR_006683 | SoftSearch - Detecting Structural Variations Using Split Reads and Discordant Read Pairs | 2026-08-01 12:03:17 | 5 | |||||||
|
GLAD Resource Report Resource Website 100+ mentions |
GLAD (RRID:SCR_001284) | GLAD | software resource | Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified. | comparative genomic hybridization, breakpoint, copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15381628 | Free, Available for download, Freely available | OMICS_02053 | SCR_001284 | GLAD - Gain and Loss Analysis of DNA, Gain and Loss Analysis of DNA | 2026-08-01 12:08:11 | 283 | ||||||
|
Bycom Resource Report Resource Website |
Bycom (RRID:SCR_000659) | software resource | A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output. | methylcytosine, bs-seq, fastq, sam, bam, snps, snp, wgbs, rrbs, sorftw |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25255082 | Free, Available for download, Freely available | OMICS_00594 | SCR_000659 | 2026-08-01 12:08:11 | 0 | ||||||||
|
VennDiagram Resource Report Resource Website 1000+ mentions |
VennDiagram (RRID:SCR_002414) | software toolkit, software resource | Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. | Venn and Euler plots, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: Debian is related to: jVenn has parent organization: CRAN |
PMID:21269502 | Free, Available for download, Freely available | OMICS_05570 | https://sources.debian.org/src/r-cran-venndiagram/ | SCR_002414 | VennDiagram: Generate high-resolution Venn and Euler plots | 2026-08-02 09:03:31 | 1811 | ||||||
|
CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software toolkit, software resource | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-08-02 09:02:51 | 31 | ||||||||
|
ProLinks Database of Functional Linkages Resource Report Resource Website |
ProLinks Database of Functional Linkages (RRID:SCR_003185) | software toolkit, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage. | functional linkage, protein linkage, inference method |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
PMID:15128449 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00580 | http://prl.mbi.ucla.edu/prlbeta/prolinks.jsp http://dip.mbi.ucla.edu/dipbeta/prolinks.jsp | SCR_003185 | Prolinks | 2026-08-02 09:03:35 | 0 | ||||||
|
metaMA Resource Report Resource Website |
metaMA (RRID:SCR_000408) | software toolkit, software resource | Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: CRAN is related to: SMAGEXP |
Scottish Government Rural and Environment Research and Analysis Directorate | PMID:19628502 | Free, Available for download, Freely available | OMICS_03524 | SCR_000408 | Meta-analysis for MicroArrays, Meta analysis for MicroArrays | 2026-08-02 09:02:51 | 0 | ||||||
|
Eigensoft Resource Report Resource Website 1000+ mentions Issue |
Eigensoft (RRID:SCR_004965) | EIGENSOFT | software toolkit, software resource | EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction. | population genetics, genetics, stratification, variation |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:17194218 DOI:10.1038/ng1847 |
OMICS_07868, nlx_93059 | https://sources.debian.org/src/eigensoft/ | http://genepath.med.harvard.edu/~reich/Software.htm | SCR_004965 | EIGENSOFT Software | 2026-08-02 09:04:06 | 1225 |
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.
