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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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UCHIME Resource Report Resource Website 1000+ mentions |
UCHIME (RRID:SCR_008057) | UCHIME | software resource | An algorithm for detecting chimeric sequences. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_01115 | SCR_008057 | 2026-02-14 02:01:32 | 1777 | ||||||||||
|
RJaCGH Resource Report Resource Website 1+ mentions |
RJaCGH (RRID:SCR_008381) | RJaCGH | software resource | Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models. | is listed by: OMICtools | GNU General Public License, v3 | OMICS_00731 | SCR_008381 | RJaCGH: Reversible Jump MCMC for the analysis of CGH arrays | 2026-02-14 02:01:41 | 1 | ||||||||
|
OnlineCall Resource Report Resource Website |
OnlineCall (RRID:SCR_008263) | OnlineCall | software resource | A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII. | is listed by: OMICtools | OMICS_01153 | SCR_008263 | 2026-02-14 02:01:35 | 0 | ||||||||||
|
IsaCGH Resource Report Resource Website |
IsaCGH (RRID:SCR_008375) | IsaCGH | software resource | Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations. | microarray, array cgh, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00727, biotools:isacgh | https://bio.tools/isacgh | SCR_008375 | 2026-02-14 02:01:41 | 0 | ||||||||
|
SeqPig Resource Report Resource Website 1+ mentions |
SeqPig (RRID:SCR_008548) | SeqPig | software resource | A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters. | mapreduce/hadoop |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24149054 | OMICS_01226 | SCR_008548 | 2026-02-14 02:01:40 | 2 | ||||||||
|
CAT Resource Report Resource Website 10+ mentions |
CAT (RRID:SCR_008421) | CAT | software resource | A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01676, biotools:CAt | https://bio.tools/CAT | SCR_008421 | 2026-02-14 02:01:38 | 13 | |||||||
|
Ultrasome Resource Report Resource Website |
Ultrasome (RRID:SCR_008465) | Ultrasome | software resource | An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data. |
is listed by: OMICtools has parent organization: Broad Institute |
PMID:19228802 | Acknowledgement requested, Free for academic use | OMICS_00737 | SCR_008465 | 2026-02-14 02:01:39 | 0 | ||||||||
|
OligoPicker Resource Report Resource Website 1+ mentions |
OligoPicker (RRID:SCR_008720) | OligoPicker | software resource | Software to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting. | is listed by: OMICtools | PMID:12724288 | GNU General Public License, Acknowledgement requested | OMICS_00830 | SCR_008720 | 2026-02-14 02:01:38 | 3 | ||||||||
|
Biodoop Resource Report Resource Website |
Biodoop (RRID:SCR_008711) | Biodoop | software resource | A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop. | mapreduce/hadoop | is listed by: OMICtools | OMICS_01224 | SCR_008711 | 2026-02-14 02:01:43 | 0 | |||||||||
|
DrGaP Resource Report Resource Website 10+ mentions |
DrGaP (RRID:SCR_008670) | DrGaP | software resource | Designed to identify Driver Genes and Pathways in cancer genome sequencing studies. | is listed by: OMICtools | Cancer | OMICS_00149 | SCR_008670 | 2026-02-14 02:01:43 | 10 | |||||||||
|
InVEx Resource Report Resource Website 1+ mentions |
InVEx (RRID:SCR_008734) | InVEx | software resource | A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00151 | SCR_008734 | Introns Vs Exons | 2026-02-14 02:01:44 | 4 | |||||||||
|
SPLINTER Resource Report Resource Website 10+ mentions |
SPLINTER (RRID:SCR_005826) | SPLINTER | software resource | Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples. |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
Cancer | Free for academic / non-profit use, Commercial use requires license | OMICS_00100 | SCR_005826 | Short IN/DEL Prediction by Large deviation Inference and Non-linear True frequency Estimation by Recursion | 2026-02-14 02:01:01 | 13 | |||||||
|
MetaQC Resource Report Resource Website 10+ mentions |
MetaQC (RRID:SCR_006000) | software resource | Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision. | standalone software, mac os x, unix/linux, windows, r, FASEB list |
is listed by: OMICtools has parent organization: CRAN |
PMID:22116060 | GNU General Public License, v2 | OMICS_04032 | https://github.com/donkang34/MetaQC | SCR_006000 | MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis, MetaQC: Objective Quality Control and Inclusion / Exclusion Criteria for Genomic Meta-Analysis | 2026-02-14 02:01:03 | 40 | ||||||
|
deepSNV Resource Report Resource Website 10+ mentions |
deepSNV (RRID:SCR_006214) | deepSNV | software resource | Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants). | data import, genetic variability, genetics, snp, sequencing, single nucleotide variant, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24443148 | GNU General Public License, v3 | OMICS_02239, biotools:deepsnv | https://bio.tools/deepsnv | SCR_006214 | deepSNV - Detection of subclonal SNVs in deep sequencing experiments | 2026-02-14 02:01:06 | 34 | |||||
|
pepStat Resource Report Resource Website 1+ mentions |
pepStat (RRID:SCR_006240) | software resource | Software for statistical analysis of peptide microarrays. It uses an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization. | standalone software | is listed by: OMICtools | PMID:23770318 | OMICS_04027 | SCR_006240 | 2026-02-14 02:01:06 | 8 | |||||||||
|
estMOI Resource Report Resource Website 10+ mentions |
estMOI (RRID:SCR_006192) | estMOI | software resource | A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt). | multiplicity of infection, parasite, genome, high throughput sequencing, single nucleotide polymorphism, chromosome | is listed by: OMICtools | PMID:24443379 | Free, Public | OMICS_02240 | SCR_006192 | estMOI - Estimating multiplicity of infection using parasite deep sequencing data | 2026-02-14 02:01:14 | 10 | ||||||
|
PhyloBayes Resource Report Resource Website 100+ mentions |
PhyloBayes (RRID:SCR_006402) | PhyloBayes | software resource | A Bayesian Monte Carlo Markov Chain (MCMC) sampler software for phylogenetic reconstruction. Its main distinguishing feature is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenomic, multigene alignment, alignment, reconstruction |
is listed by: OMICtools has parent organization: University of Montreal; Quebec; Canada |
PMID:24318999 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02212 | SCR_006402 | PhyloBayes - phylogenetic reconstruction using infinite mixtures | 2026-02-14 02:01:09 | 485 | ||||||
|
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 | 2026-02-14 02:01:18 | 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 | 2026-02-14 02:01:09 | 7 | |||||
|
NGS tools for the novice Resource Report Resource Website 1+ mentions |
NGS tools for the novice (RRID:SCR_000664) | NGS tools for the novice | software resource | A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution. | next generation sequencing, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01063 | SCR_000664 | NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data | 2026-02-14 01:59:47 | 3 |
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