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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CATALYSTLite Resource Report Resource Website |
CATALYSTLite (RRID:SCR_017126) | analysis service resource, data analysis service, production service resource, service resource | Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package. | interactive, Shiny, website, application, interface, mass, cytometry, data, processing, pipeline |
is used by: CATALYST is related to: Bioconductor has parent organization: University of Zurich; Zurich; Switzerland |
Free, Freely available | SCR_017126 | 2026-09-12 01:02:17 | 0 | ||||||||||
|
rbsurv Resource Report Resource Website 1+ mentions |
rbsurv (RRID:SCR_001175) | rbsurv | software resource | Software package that selects genes associated with survival. | microarray, gene, survival, 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 | biotools:rbsurv, BioTools:rbsurv, OMICS_02088 | https://bio.tools/rbsurv, https://bio.tools/rbsurv, https://bio.tools/rbsurv | SCR_001175 | rbsurv - Robust likelihood-based survival modeling with microarray data | 2026-09-12 12:55:20 | 1 | ||||||
|
wateRmelon Resource Report Resource Website 100+ mentions |
wateRmelon (RRID:SCR_001296) | wateRmelon | software resource | Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages. | dna methylation, microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23631413 | Free, Available for download, Freely available | OMICS_02039, biotools:watermelon | https://bio.tools/watermelon | SCR_001296 | 2026-09-12 12:55:23 | 314 | ||||||
|
spotSegmentation Resource Report Resource Website |
spotSegmentation (RRID:SCR_001298) | spotSegmentation | data processing software, image processing software, software application, 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 | 2026-09-12 12:55:23 | 0 | ||||||
|
ARRmNormalization Resource Report Resource Website |
ARRmNormalization (RRID:SCR_001292) | ARRmNormalization | software resource | Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay. | dna methylation, microarray, preprocessing, two channel, illumina |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02044 | SCR_001292 | ARRmNormalization - Adaptive Robust Regression normalization for Illumina methylation data | 2026-09-12 12:55:23 | 0 | |||||||
|
GeneMeta Resource Report Resource Website 1+ mentions |
GeneMeta (RRID:SCR_001201) | GeneMeta | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:55:21 | 1 | |||||||
|
methylMnM Resource Report Resource Website 1+ mentions |
methylMnM (RRID:SCR_001289) | methylMnM | software resource | Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison. | dna methylation, sequencing, medip-seq, mre-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v3 | OMICS_02047 | SCR_001289 | methylMnM - detect different methylation level (DMR) | 2026-09-12 12:55:23 | 9 | |||||||
|
metahdep Resource Report Resource Website |
metahdep (RRID:SCR_001225) | metahdep | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:55:21 | 0 | |||||
|
categoryCompare Resource Report Resource Website 1+ mentions |
categoryCompare (RRID:SCR_001223) | categoryCompare | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:55:21 | 9 | ||||||
|
MergeMaid Resource Report Resource Website 1+ mentions |
MergeMaid (RRID:SCR_001221) | MergeMaid | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival. | differential expression, microarray, visualization, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16646808 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02124 | SCR_001221 | Merge Maid | 2026-09-12 12:55:21 | 3 | ||||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-12 12:55:22 | 31 | ||||||
|
iterativeBMAsurv Resource Report Resource Website |
iterativeBMAsurv (RRID:SCR_001254) | iterativeBMAsurv | software resource | Software package providing a variable selection method for applying survival analysis to microarray data. | microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19245714 | GNU General Public License, v2 or newer | OMICS_02086 | SCR_001254 | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis, iterativeBMAsurv - The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis | 2026-09-12 12:55:22 | 0 | ||||||
|
snpStats: SnpMatrix and XSnpMatrix classes and methods Resource Report Resource Website 50+ mentions |
snpStats: SnpMatrix and XSnpMatrix classes and methods (RRID:SCR_001249) | snpStats | software resource | Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies. | r, single nucleotide polymorphism, genetic variability, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:16720584 | Free, Available for download, Freely available | OMICS_02091 | SCR_001249 | 2026-09-12 12:55:22 | 79 | |||||||
|
exomeCopy Resource Report Resource Website 10+ mentions |
exomeCopy (RRID:SCR_001276) | exomeCopy | software resource | Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count. | copy number variation, genetics, sequencing, exome |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23089826 | Free, Available for download, Freely available | OMICS_02062 | http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html | SCR_001276 | exomeCopy - Copy number variant detection from exome sequencing read depth | 2026-09-12 12:55:22 | 16 | |||||
|
SMAP Resource Report Resource Website 100+ mentions |
SMAP (RRID:SCR_001270) | SMAP | software resource | Software package providing functions and classes for DNA copy number profiling of array-CGH data. | copy number variation, microarray, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18204059 | Free, Available for download, Freely available | OMICS_02068 | SCR_001270 | SMAP - A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling | 2026-09-12 12:55:22 | 210 | ||||||
|
SNAGEE Resource Report Resource Website |
SNAGEE (RRID:SCR_001301) | SNAGEE | software resource | Software package that uses signal-to-noise ratios (SNRs) as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set. | microarray, one channel, quality control, two channel, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23251415 | Free, Available for download, Freely available | OMICS_02035 | SCR_001301 | Signal-to-Noise applied to Gene Expression Experiments | 2026-09-12 12:55:23 | 0 | ||||||
|
MinimumDistance Resource Report Resource Website |
MinimumDistance (RRID:SCR_001260) | MinimumDistance | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:55:22 | 0 | |||||||
|
factDesign Resource Report Resource Website |
factDesign (RRID:SCR_001330) | factDesign | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:55:24 | 0 | ||||||
|
pickgene Resource Report Resource Website |
pickgene (RRID:SCR_001331) | pickgene | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:55:24 | 0 | |||||||
|
oneChannelGUI Resource Report Resource Website 10+ mentions |
oneChannelGUI (RRID:SCR_001325) | oneChannelGUI | software resource | Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, rna-seq, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:17875544 | Free, Available for download, Freely available | biotools:onechannelgu, OMICS_02004 | http://www.bioconductor.org/packages/release/bioc/html/oneChannelGUI.html | SCR_001325 | 2026-09-12 12:55:24 | 13 |
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