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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | data processing software, data analysis software, software resource, software application, software toolkit | Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff. | copy number variation analysis, copy number variation, microarray, affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:21486749 | Free, Available for download, Freely available | biotools:cn.farms, OMICS_02060 | https://bio.tools/cn.farms | SCR_000289 | cn.farms - factor analysis for copy number estimation | 2026-08-04 09:40:06 | 0 | |||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | data processing software, data analysis software, software resource, sequence analysis software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. | sequencing, correlated mutation, selection pressure, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: CRAN has parent organization: Bioconductor |
PMID:24681904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03636, biotools:cormut | https://bio.tools/cormut | SCR_000053 | CorMut - Detect the correlated mutations based on selection pressure | 2026-08-04 09:40:02 | 0 | ||||||
|
metaSeq Resource Report Resource Website |
metaSeq (RRID:SCR_000056) | metaSeq | data processing software, software application, software resource, data analysis software | Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method. | differential expression, rna-seq, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02123 | SCR_000056 | 2026-08-04 09:40:03 | 0 | ||||||||
|
GeneMeta Resource Report Resource Website 1+ mentions |
GeneMeta (RRID:SCR_001201) | GeneMeta | data processing software, software application, software resource, data analysis software | Software package providing a collection of meta-analysis tools for analysing high throughput experimental data. | sequencing, high throughput |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02120 | SCR_001201 | GeneMeta - MetaAnalysis for High Throughput Experiments | 2026-08-04 09:40:20 | 1 | |||||||
|
Starr Resource Report Resource Website |
Starr (RRID:SCR_001071) | data processing software, software application, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences. | data import, quality, visualization, r, genomics, mapping, data analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20398407 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00811 | SCR_001071 | 2026-08-04 09:40:18 | 0 | ||||||||
|
metahdep Resource Report Resource Website |
metahdep (RRID:SCR_001225) | metahdep | data processing software, software application, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies. | differential expression, microarray, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19648140 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:metahdep, OMICS_02121 | https://bio.tools/metahdep | SCR_001225 | metahdep - Hierarchical Dependence in Meta-Analysis | 2026-08-04 09:40:20 | 0 | |||||
|
categoryCompare Resource Report Resource Website 1+ mentions |
categoryCompare (RRID:SCR_001223) | categoryCompare | data processing software, software application, software resource, data analysis software | A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested). | annotation, go, gene expression, multiple comparison, pathway, gene |
uses: Cytoscape is listed by: OMICtools is related to: Gene Ontology is related to: CRAN has parent organization: Bioconductor |
PMID:24808906 | Free, Available for download, Freely available | OMICS_02122 | SCR_001223 | categoryCompare - Meta-analysis of high-throughput experiments using feature annotations | 2026-08-04 09:40:20 | 9 | ||||||
|
BAC Resource Report Resource Website |
BAC (RRID:SCR_001067) | BAC | data processing software, data analysis software, software resource, sequence analysis software, software application | R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments. | software, bayesian, chip, hierarchy, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00801 | SCR_001067 | 2026-08-04 09:40:17 | 0 | ||||||||
|
targetscan.Hs.eg.db Resource Report Resource Website |
targetscan.Hs.eg.db (RRID:SCR_001068) | data processing software, data analysis software, software resource, sequence analysis software, software application | R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. | software, biological targets, mirna, prediction, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00790 | SCR_001068 | 2026-08-04 09:40:18 | 0 | |||||||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | data processing software, data analysis software, software resource, sequence analysis software, software application | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-08-04 09:40:21 | 30 | ||||||
|
rGADEM Resource Report Resource Website |
rGADEM (RRID:SCR_001091) | data processing software, data analysis software, software resource, sequence analysis software, software application | R package with tools for de novo motif discovery in large-scale genomic sequence data. | de novo motif, genomics, sequencing, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00491 | SCR_001091 | 2026-08-04 09:40:18 | 0 | |||||||||
|
MinimumDistance Resource Report Resource Website |
MinimumDistance (RRID:SCR_001260) | MinimumDistance | data processing software, software application, software resource, data analysis software | Software package for analysis of de novo copy number variants in trios from high-dimensional genotyping platforms. | copy number variation, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02066 | SCR_001260 | MinimumDistance - A package for de novo CNV detection in case-parent trios | 2026-08-04 09:40:21 | 0 | |||||||
|
factDesign Resource Report Resource Website |
factDesign (RRID:SCR_001330) | factDesign | data processing software, software application, software resource, data analysis software | Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. | microarray, differential expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18584033 | Free, Available for download, Freely available | OMICS_02008 | SCR_001330 | factDesign - Factorial designed microarray experiment analysis | 2026-08-04 09:40:21 | 0 | ||||||
|
spotSegmentation Resource Report Resource Website |
spotSegmentation (RRID:SCR_001298) | spotSegmentation | data processing software, software application, image processing software, software resource | Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three. | gridding, segmentation, microarray, preprocessing, quality control, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15845656 | Free, Available for download, Freely available | OMICS_02037 | http://www.bioconductor.org/packages/release/bioc/html/spotSegmentation.html | SCR_001298 | 2026-08-04 09:40:21 | 0 | ||||||
|
pickgene Resource Report Resource Website |
pickgene (RRID:SCR_001331) | pickgene | data processing software, software application, software resource, data analysis software | Software for adaptive Gene Picking for Microarray Expression Data Analysis. | microarray, gene expression, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02007, biotools:pickgene | https://bio.tools/pickgene | SCR_001331 | 2026-08-04 09:40:21 | 0 | |||||||
|
genArise Resource Report Resource Website 10+ mentions |
genArise (RRID:SCR_001346) | genArise | data processing software, software application, software resource, data analysis software | An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely Available | OMICS_01993 | SCR_001346 | genArise - Microarray Analysis tool | 2026-08-04 09:40:21 | 22 | |||||||
|
plateCore Resource Report Resource Website |
plateCore (RRID:SCR_001743) | software resource, database, data or information resource | Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956418 | Free, Available for download, Freely available | OMICS_05641 | http://www.bioconductor.org/packages/release/bioc/html/plateCore.html | SCR_001743 | plateCore - Statistical tools and data structures for plate-based flow cytometry | 2026-08-04 09:40:27 | 0 | ||||||
|
asSeq Resource Report Resource Website 1+ mentions |
asSeq (RRID:SCR_001625) | asSeq | data processing software, source code, data analysis software, software resource, software application | Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq | r, rna-seq, expression quantitative trait locus, total read count, allele-specific expression, allele-specific gene expression, gene expression quantitative trait locus, rna isoform, gene expression, genetic marker, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bioconductor has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21838806 | Free, Available for download, Freely available | OMICS_01948, nlx_153893, biotools:asseq | https://bio.tools/asseq | SCR_001625 | 2026-08-04 09:40:25 | 6 | ||||||
|
GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | data processing software, software application, software resource, data analysis software | Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. | compare, group, sample, gene, expression, omnibus, data, identify, differentially, expressed, across, condition, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: GEOquery is related to: LIMMA |
Free, Available for download, Freely available | biotools:GEO2R | https://bio.tools/GEO2R | SCR_016569 | 2026-08-04 09:43:56 | 58 | ||||||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research (CIHR) and Genome BC ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | VisRseq, VisR | 2026-08-04 09:43:58 | 5 |
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