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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Array Studio Resource Report Resource Website 1+ mentions |
Array Studio (RRID:SCR_010970) | data processing software, analysis service resource, data analysis software, production service resource, service resource, software toolkit, software application, software resource | Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data. | Statistic, visualization, data, analysis, quantification, integrated environment, microarray data, RTPCR data, Taqman data, genotype data, copy number data, next generation sequencing data | Free, Available for download, Freely available | OMICS_00850 | https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/ArrayStudio/ArrayStudio/ | http://www.omicsoft.com/array-studio.php | SCR_010970 | 2026-02-14 02:02:08 | 5 | ||||||||
|
HMCan Resource Report Resource Website 10+ mentions |
HMCan (RRID:SCR_010858) | HMCan | software resource | A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:24021381 | biotools:hmcan, OMICS_00443 | https://bio.tools/hmcan | SCR_010858 | Histone Modification in Cancer | 2026-02-14 02:02:06 | 13 | ||||||
|
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 | |||||
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, software resource, data processing software, software application | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool https://bio.tools/limma https://sources.debian.org/src/r-bioc-limma/ |
SCR_010943 | Linear Models for Microarray Data | 2026-02-14 02:02:08 | 24583 | ||||||
|
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 | ||||||||||
|
FISH Oracle Resource Report Resource Website |
FISH Oracle (RRID:SCR_010927) | FISH Oracle | data or information resource, software resource, database | A web-based software tool for the integrative analysis of cancer genomics data. It stores different kinds of downstream processed data from multiple samples in a single database. A powerful search interface allows to dynamically filter the data to be displayed with respect to different criteria. The combination of AJAX technology and a fast visualization engine facilitates a highly dynamic visualization for large amounts of data. FISH Oracle 2 is able to simultaneously display different data sets, thus simplifying their comparison. Filter and display options can be changed on the fly. High quality image export enables the life scientist to easily communicate the results, e.g. in presentations or publications. A comprehensive data administration assures to keep track of the data stored in the database. | array cgh, snp, genomics, visualization |
is listed by: OMICtools has parent organization: University of Hamburg; Hamburg; Germany |
Cancer | PMID:21884636 | OMICS_00721 | SCR_010927 | 2026-02-14 02:02:08 | 0 | |||||||
|
oPOSSUM Resource Report Resource Website 100+ mentions |
oPOSSUM (RRID:SCR_010884) | oPOSSUM | data analysis service, analysis service resource, production service resource, service resource, software resource | A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences. | transcription factor binding site | is listed by: OMICtools | PMID:22973536 PMID:17576675 PMID:15933209 |
Acknowledgement requested | OMICS_00488 | SCR_010884 | oPOSSUM-3 | 2026-02-14 02:02:06 | 101 | ||||||
|
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 |
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