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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
COPS Resource Report Resource Website 100+ mentions |
COPS (RRID:SCR_010852) | COPS | software resource | Software for detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets. |
is listed by: OMICtools has parent organization: Heidelberg University; Baden-Wurttemberg; Germany |
PMID:23272209 | OMICS_00479 | SCR_010852 | COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets | 2026-02-14 02:02:05 | 267 | ||||||||
|
GenomeStudio Resource Report Resource Website 1000+ mentions |
GenomeStudio (RRID:SCR_010973) | GenomeStudio | software resource | Visualize and analyze data generated by all of Illumina''s platforms. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00854 | SCR_010973 | 2026-02-14 02:02:07 | 2954 | ||||||||||
|
ComBat Resource Report Resource Website 1000+ mentions |
ComBat (RRID:SCR_010974) | ComBat | software resource | Adjusting batch effects in microarray expression data using Empirical Bayes methods. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00857 | SCR_010974 | 2026-02-14 02:02:09 | 3492 | ||||||||||
|
MicroGen Resource Report Resource Website 10+ mentions |
MicroGen (RRID:SCR_010976) | MicroGen | software resource | Software application package for a Minimum Information About Microarray Experiments (MIAME) compliant web-based information system for managing all the information completely characterizing spotted microarray experiments and the produced data. | microarray |
is listed by: OMICtools has parent organization: Polytechnic University of Milan; Milan; Italy |
PMID:16351755 | OMICS_00867 | SCR_010976 | MicroGen - a Web Server for Microarray Experiments | 2026-02-14 02:01:52 | 34 | |||||||
|
E-RANGE Resource Report Resource Website |
E-RANGE (RRID:SCR_010856) | E-RANGE | software resource | A Python package for doing RNA-seq and ChIP-seq (hence the dual-use). | is listed by: OMICtools | OMICS_00439 | SCR_010856 | 2026-02-14 02:01:50 | 0 | ||||||||||
|
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 | ||||||||
|
BioTile Resource Report Resource Website |
BioTile (RRID:SCR_010953) | BioTile | software resource | A Perl based tool for the identification of differentially enriched regions in tiling microarray data. | is listed by: OMICtools | OMICS_00791 | SCR_010953 | 2026-02-14 02:02:07 | 0 | ||||||||||
|
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 | ||||||||||
|
CNA-HMMer Resource Report Resource Website |
CNA-HMMer (RRID:SCR_010924) | CNA-HMMer | software resource | A software for detection of DNA copy number alterations (CNAs) from array comparative genomic hybridization (aCGH) data. |
is listed by: OMICtools has parent organization: University of British Columbia; British Columbia; Canada |
OMICS_00714 | SCR_010924 | 2026-02-14 02:02:07 | 0 | ||||||||||
|
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 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
Email: info_at_ dknet.org
