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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-14 02:02:15 | 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 | 2026-02-14 02:02:21 | 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 | 2026-02-14 02:02:45 | 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 | 2026-02-14 02:02:16 | 0 | ||||||||
|
MotifLab Resource Report Resource Website 1+ mentions |
MotifLab (RRID:SCR_012649) | MotifLab | software resource | Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. |
is listed by: OMICtools has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
Research Council of Norway | PMID:23323883 | Acknowledgement requested, Free, Public | OMICS_00486 | SCR_012649 | 2026-02-14 02:02:15 | 2 | |||||||
|
tRanslatome Resource Report Resource Website 1+ mentions |
tRanslatome (RRID:SCR_012810) | tRanslatome | software resource | Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24222209 | Free | OMICS_01316 | SCR_012810 | tRanslatome - Comparison between multiple levels of gene expression | 2026-02-14 02:02:47 | 2 | |||||||
|
BEDOPS Resource Report Resource Website 100+ mentions |
BEDOPS (RRID:SCR_012865) | BEDOPS | software resource | A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets. |
is listed by: OMICtools is listed by: Debian |
PMID:22576172 DOI:10.1093/bioinformatics/bts277 |
GNU General Public License, v3 | OMICS_00949 | https://sources.debian.org/src/bedops/ | SCR_012865 | BEDOPS: high-performance genomic feature operations | 2026-02-14 02:02:24 | 220 | ||||||
|
featureCounts Resource Report Resource Website 10000+ mentions |
featureCounts (RRID:SCR_012919) | featureCounts | software resource | A read summarization program, which counts mapped reads for the genomic features such as genes and exons. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is required by: SL-quant |
PMID:24227677 | biotools:featurecounts, OMICS_01160 | https://bio.tools/featurecounts | SCR_012919 | featureCounts: a universal read summarization program | 2026-02-14 02:02:48 | 12197 | ||||||
|
BicARE Resource Report Resource Website |
BicARE (RRID:SCR_012881) | BicARE | software resource | Biclustering Analysis and Results Exploration. |
is listed by: OMICtools has parent organization: Bioconductor |
Free | OMICS_01803 | SCR_012881 | 2026-02-14 02:02:44 | 0 | |||||||||
|
dmrFinder Resource Report Resource Website 10+ mentions |
dmrFinder (RRID:SCR_012853) | dmrFinder | software resource | Function for differentially methylated regions (DMR) detection that is a part of the charm package in R/Bioconductor. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00621 | SCR_012853 | 2026-02-14 02:02:24 | 27 | ||||||||||
|
ChIPpeakAnno Resource Report Resource Website 100+ mentions |
ChIPpeakAnno (RRID:SCR_012828) | ChIPpeakAnno | software resource | Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00804 | SCR_012828 | 2026-02-14 02:02:17 | 448 | ||||||||||
|
inSilicoMerging Resource Report Resource Website 10+ mentions |
inSilicoMerging (RRID:SCR_012829) | inSilicoMerging | software resource | Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00859 | SCR_012829 | 2026-02-14 02:02:43 | 37 | ||||||||||
|
DEXSeq Resource Report Resource Website 500+ mentions |
DEXSeq (RRID:SCR_012823) | DEXSeq | software resource | Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
OMICS_01329, biotools:dexseq | https://bio.tools/dexseq | SCR_012823 | 2026-02-14 02:02:23 | 506 | ||||||||
|
snapCGH Resource Report Resource Website 1+ mentions |
snapCGH (RRID:SCR_012947) | snapCGH | software resource | Software providing methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00734 | SCR_012947 | 2026-02-14 02:02:48 | 5 | ||||||||||
|
ArrayTrack Resource Report Resource Website 50+ mentions |
ArrayTrack (RRID:SCR_012839) | ArrayTrack | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. |
uses: Gene Ontology For Functional Analysis (GOFFA) is listed by: OMICtools has parent organization: U.S. Food and Drug Administration |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00851 | SCR_012839 | 2026-02-14 02:02:23 | 66 | |||||||||
|
miRNApath Resource Report Resource Website 1+ mentions |
miRNApath (RRID:SCR_012833) | miRNApath | software resource | Software package that provides pathway enrichment techniques for miRNA expression data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00787 | SCR_012833 | 2026-02-14 02:02:44 | 4 | ||||||||||
|
RepeatMasker Resource Report Resource Website 5000+ mentions |
RepeatMasker (RRID:SCR_012954) | software resource | Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ). |
uses: Repbase uses: RMBlast is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
DOI:10.1007/978-1-61779-603-6_2 | nlx_156840, OMICS_09436 | https://sources.debian.org/src/repeatmasker/ | SCR_012954 | repeatmasker.org | 2026-02-14 02:02:48 | 9750 | ||||||||
|
sva package Resource Report Resource Website 50+ mentions |
sva package (RRID:SCR_012836) | sva package | software resource | Contains functions for removing batch effects and other unwanted variation in high-throughput experiment. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00861 | SCR_012836 | Surrogate Variable Analysis | 2026-02-14 02:02:17 | 82 | |||||||||
|
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 | 2026-02-14 02:02:47 | 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 | 2026-02-14 02:02:48 | 106 |
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