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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
FindPeaks Resource Report Resource Website 100+ mentions |
FindPeaks (RRID:SCR_010857) | FindPeaks | software resource | Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis). | chip-seq |
is listed by: OMICtools has parent organization: SourceForge |
BC Cancer Agency ; Michael Smith Foundation for Health Research |
OMICS_00440 | SCR_010857 | 2026-02-14 02:02:05 | 328 | ||||||||
|
CoCo Resource Report Resource Website 500+ mentions |
CoCo (RRID:SCR_010947) | CoCo | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2021.A computational tool that allows the user to search, visualise and store different data associated with gene expression. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:17234641 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00805, biotools:CoCo | https://bio.tools/CoCo | SCR_010947 | ChIP-on-chip online | 2026-02-14 02:02:08 | 978 | |||||
|
Mayday Resource Report Resource Website 10+ mentions |
Mayday (RRID:SCR_010945) | Mayday | software resource | Software providing a workbench for visualization, analysis and storage of microarray data. It features a graphical user interface and supports the development and integration of existing and new analysis methods. Besides the infrastructural core functionality, Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases, and different clustering methods, including phylogenetic methods. In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources. This meta information can be used to enhance visualizations, such as in the enhanced heatmap visualization. Written in the Java programming language, Mayday is extremely portable and runs on all platforms supporting the Java runtime environment 1.6. | java |
is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
GNU General Public License, Plug-ins:, GNU Lesser General Public License | OMICS_00773 | SCR_010945 | Mayday - Microarray Data Analysis | 2026-02-14 02:02:07 | 14 | |||||||
|
RPPanalyzer Resource Report Resource Website 1+ mentions |
RPPanalyzer (RRID:SCR_010959) | RPPanalyzer | software resource | A statistical tool developed to read reverse-phase protein array data, to perform the basic data analysis and to visualize the resulting biological information. | is listed by: OMICtools | GNU Lesser General Public License, v2, 2.1, 3 | OMICS_00815 | SCR_010959 | RPPanalyzer: Reads annotates and normalizes reverse phase protein array data | 2026-02-14 02:02:08 | 8 | ||||||||
|
IMA Resource Report Resource Website 1+ mentions |
IMA (RRID:SCR_010955) | IMA | software resource | A software package designed to automate the pipeline for analyzing site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray. | is listed by: OMICtools | OMICS_00795 | SCR_010955 | 2026-02-14 02:02:08 | 6 | ||||||||||
|
TFBSGroup Resource Report Resource Website 1+ mentions |
TFBSGroup (RRID:SCR_010887) | TFBSGroup | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A Software program for Predicting Transcription Factor Binding Sites. | transcription factor binding site | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00494 | SCR_010887 | TFBSGroup: A Program for Predicting Transcription Factor Binding Sites | 2026-02-14 02:01:51 | 1 | |||||||
|
CGH Explorer Resource Report Resource Website 1+ mentions |
CGH Explorer (RRID:SCR_010920) | CGH Explorer | software resource | An easy-to-use software tool for analyzing two color copy number alteration arrays from multiple platforms, including Agilent Technologies, Illumina, AffyMetrix, NimbleGen and others. | is listed by: OMICtools | Commercially available | OMICS_00708 | SCR_010920 | 2026-02-14 02:02:07 | 2 | |||||||||
|
CGHPRO Resource Report Resource Website 1+ mentions |
CGHPRO (RRID:SCR_010921) | CGHPRO | software resource | A software for the analysis and visualization of array CGH data. | is listed by: OMICtools | PMID:15807904 | OMICS_00711 | SCR_010921 | 2026-02-14 02:02:08 | 1 | |||||||||
|
CGHseg Resource Report Resource Website 1+ mentions |
CGHseg (RRID:SCR_010922) | CGHseg | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Software R package dedicated to the analysis of CGH profiles using segmentation models. | is listed by: OMICtools | PMID:21209153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00712 | SCR_010922 | 2026-02-14 02:01:51 | 1 | ||||||||
|
NPS Resource Report Resource Website 100+ mentions |
NPS (RRID:SCR_010890) | NPS | software resource | A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: iNPS has parent organization: Dana-Farber Cancer Institute |
PMID:19014516 | OMICS_00505, biotools:nps | https://bio.tools/nps | SCR_010890 | Nucleosome Positioning from Sequencing, NPS (Nucleosome Positioning from Sequencing) | 2026-02-14 02:02:07 | 121 | ||||||
|
BASE Resource Report Resource Website 500+ mentions |
BASE (RRID:SCR_010937) | BASE | software resource | A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Lund University; Lund; Sweden |
PMID:19822003 | GNU General Public License, v3 | OMICS_00749 | SCR_010937 | BASE - BioArray Software Environment, BioArray Software Environment | 2026-02-14 02:02:07 | 506 | |||||||
|
BRB-ArrayTools Resource Report Resource Website 500+ mentions |
BRB-ArrayTools (RRID:SCR_010938) | BRB-ArrayTools | software resource | An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., 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 is listed by: SoftCite has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00750, biotools:brb-arraytools | https://bio.tools/brb-arraytools | SCR_010938 | 2026-02-14 02:02:08 | 569 | |||||||
|
nucleR Resource Report Resource Website 10+ mentions |
nucleR (RRID:SCR_010895) | nucleR | software resource | A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Barcelona; Barcelona; Spain |
PMID:21653521 | OMICS_00511, biotools:nucler | https://bio.tools/nucler | SCR_010895 | 2026-02-14 02:02:06 | 27 | |||||||
|
Genovar Resource Report Resource Website 1+ mentions |
Genovar (RRID:SCR_010930) | Genovar | software resource | A Detection and Visualization software tool for Genomic Variants. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Korea National Institute of Health |
Free, Public | OMICS_00724, biottools:genovar | https://bio.tools/genovar | SCR_010930 | 2026-02-14 02:02:07 | 1 | |||||||
|
MAnorm Resource Report Resource Website 100+ mentions |
MAnorm (RRID:SCR_010869) | MAnorm | software resource | A robust software package for quantitative comparison of ChIP-Seq data sets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute |
PMID:22424423 | OMICS_00467, biotools:manorm | https://bio.tools/manorm | SCR_010869 | Manorm - a robust model for quantitative comparison of ChIP-Seq data sets | 2026-02-14 02:01:51 | 111 | ||||||
|
mCarts Resource Report Resource Website 1+ mentions |
mCarts (RRID:SCR_010902) | mCarts | software resource | A hidden Markov model (HMM)-based software to predict clusters RNA motif sites. |
is listed by: OMICtools has parent organization: Columbia University; New York; USA |
PMID:23685613 | Apache License | OMICS_00567 | SCR_010902 | 2026-02-14 02:02:06 | 4 | ||||||||
|
MeRIP-PF Resource Report Resource Website 1+ mentions |
MeRIP-PF (RRID:SCR_010904) | MeRIP-PF | software resource | A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:merip-pf, OMICS_00571 | https://bio.tools/merip-pf | SCR_010904 | MeRIP-Seq Peak-Finding Program | 2026-02-14 02:02:07 | 3 | |||||||
|
BatMeth Resource Report Resource Website 1+ mentions |
BatMeth (RRID:SCR_010906) | BatMeth | software resource | Improved mapper for bisulfite sequencing reads on DNA methylation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
biotools:batmeth, OMICS_00574 | https://bio.tools/batmeth | SCR_010906 | 2026-02-14 02:02:06 | 1 | ||||||||
|
QUMA Resource Report Resource Website 100+ mentions |
QUMA (RRID:SCR_010907) | QUMA | software resource | You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00588, biotools:quma | https://bio.tools/quma | SCR_010907 | QUantification tool for Methylation Analysis | 2026-02-14 02:02:06 | 364 | |||||||
|
NEXT-peak Resource Report Resource Website 1+ mentions |
NEXT-peak (RRID:SCR_010862) | NEXT-peak | software resource | A software program to call peaks from ChIP-seq data for transcription factor binding sites. |
is listed by: OMICtools has parent organization: Old Dominion University; Virginia; USA |
PMID:23706083 | OMICS_00450 | SCR_010862 | 2026-02-14 02:02:05 | 1 |
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