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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DEDS Resource Report Resource Website 10+ mentions |
DEDS (RRID:SCR_001339) | DEDS | software resource | Software library that contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements methodology (Differential Expression via Distance Summary) which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach. | differential expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02002 | http://www.bioconductor.org/packages/release/bioc/html/DEDS.html | SCR_001339 | Differential Expression via Distance Summary, Differential Expression via Distance Summary for Microarray Data | 2026-09-03 04:44:41 | 15 | ||||||
|
virtualArray Resource Report Resource Website 1+ mentions |
virtualArray (RRID:SCR_001361) | virtualArray | software resource | Software package that permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analyzing the resulting virtual array. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Leipzig; Saxony; Germany |
PMID:23452776 | Free, Available for download, Freely available | OMICS_01979 | http://www.bioconductor.org/packages/release/bioc/html/virtualArray.html | SCR_001361 | 2026-09-03 04:44:34 | 5 | ||||||
|
stepNorm Resource Report Resource Website |
stepNorm (RRID:SCR_001359) | stepNorm | software resource | Software for stepwise normalization functions for cDNA microarray data. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of California at San Francisco; California; USA |
PMID:16646857 | Free, Available for download, Freely available | OMICS_01981 | SCR_001359 | stepNorm - Stepwise normalization functions for cDNA microarrays | 2026-09-03 04:44:36 | 0 | ||||||
|
RAMA Resource Report Resource Website 50+ mentions |
RAMA (RRID:SCR_001358) | RAMA | software resource | Software package for robust estimation of cDNA microarray intensities with replicates. It uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or newer | OMICS_01982 | SCR_001358 | Robust Analysis of MicroArrays | 2026-09-03 04:44:42 | 66 | |||||||
|
MANOR Resource Report Resource Website 10+ mentions |
MANOR (RRID:SCR_001305) | MANOR | software resource | Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments. | copy number variation, data import, microarray, preprocessing, quality control, two channel, comparative genomic hybridization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02028 | SCR_001305 | CGH Micro-Array NORmalization | 2026-09-03 04:44:37 | 17 | |||||||
|
dyebias Resource Report Resource Website |
dyebias (RRID:SCR_001308) | dyebias | software resource | Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias. | microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:17623705 | GNU General Public License, v3 | biotools:dyebias, OMICS_02025 | https://bio.tools/dyebias | SCR_001308 | dyebias - The GASSCO method for correcting for slide-dependent gene-specific dye bias | 2026-09-03 04:44:30 | 0 | |||||
|
limmaGUI Resource Report Resource Website 10+ mentions |
limmaGUI (RRID:SCR_001306) | limmaGUI | software resource | Software package for a Graphical User Interface for the limma Microarray package. | differential expression, gui, microarray, multiple comparison, 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:15297296 | Free, Available for download, Freely available | OMICS_02027, biotools:limmagui | https://bio.tools/limmagui | SCR_001306 | limmaGUI - GUI for limma package | 2026-09-03 04:44:31 | 14 | |||||
|
ffpe Resource Report Resource Website 500+ mentions |
ffpe (RRID:SCR_001307) | ffpe | software resource | Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots). | formalin-fixed, paraffin-embedded, gene expression, microarray, quality control, 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_02026, biotools:ffpe | https://bio.tools/ffpe | SCR_001307 | ffpe - Quality assessment and control for FFPE microarray expression data | 2026-09-03 04:44:27 | 524 | ||||||
|
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 | 2026-09-03 04:44:27 | 0 | ||||||
|
asSeq Resource Report Resource Website 1+ mentions |
asSeq (RRID:SCR_001625) | asSeq | data analysis software, data processing software, software application, software resource, source code | 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 | 2026-09-03 04:44:48 | 6 | ||||||
|
ACME Resource Report Resource Website 50+ mentions |
ACME (RRID:SCR_001464) | ACME | software resource | A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. | microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:16939795 | Free, Available for download, Freely available | OMICS_01976 | SCR_001464 | Algorithms for Calculating Microarray Enrichment | 2026-09-03 04:44:36 | 62 | ||||||
|
CoGAPS Resource Report Resource Website 10+ mentions |
CoGAPS (RRID:SCR_001479) | CoGAPS | software resource | Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets. | gene expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20810601 | Free, Available for download, Freely available | OMICS_01973 | SCR_001479 | Coordinated Gene Activity in Pattern Sets | 2026-09-03 04:44:39 | 38 | ||||||
|
flowFP Resource Report Resource Website 1+ mentions |
flowFP (RRID:SCR_001537) | software resource | A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956416 | Free, Available for download, Freely available | OMICS_05599 | SCR_001537 | flowFP - Fingerprinting for Flow Cytometry | 2026-09-03 04:44:53 | 4 | |||||||
|
ArrayExpress (R) Resource Report Resource Website 1+ mentions |
ArrayExpress (R) (RRID:SCR_000120) | ArrayExpress (R) | software resource | Software to access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet | microarray |
is listed by: OMICtools is related to: ArrayExpress has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:19505942 | Free, Available for download, Freely available | OMICS_01974 | SCR_000120 | 2026-09-03 04:43:15 | 1 | |||||||
|
AffyRNADegradation Resource Report Resource Website |
AffyRNADegradation (RRID:SCR_000118) | AffyRNADegradation | software resource | Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation. | rna degradation, gene expression, microarray, preprocessing, affymetrix, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: University of Leipzig; Saxony; Germany |
PMID:23097420 | Free, Available for download, Freely available | OMICS_01975, biotools:affyrnadegradation | https://bio.tools/affyrnadegradation | SCR_000118 | 2026-09-03 04:43:15 | 0 | ||||||
|
VariantAnnotation Resource Report Resource Website 1+ mentions |
VariantAnnotation (RRID:SCR_000074) | VariantAnnotation | software resource | Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes. | annotation, genetic variant, data import, genetics, high throughput sequencing, snp, sequencing |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor has parent organization: Fred Hutchinson Cancer Center |
PMID:24681907 | Free, Available for download, Freely available | OMICS_02073 | SCR_000074 | VariantAnnotation - Annotation of Genetic Variants | 2026-09-03 04:43:09 | 9 | ||||||
|
timecourse Resource Report Resource Website 1+ mentions |
timecourse (RRID:SCR_000077) | timecourse | software resource | Software functions for data analysis and graphical displays for developmental microarray time course data. | microarray, differential expression, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: CRAN has parent organization: Bioconductor has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | OMICS_01980, biotools:timecourse | https://bio.tools/timecourse | SCR_000077 | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-09-03 04:43:09 | 5 | ||||||
|
ncdfFlow Resource Report Resource Website |
ncdfFlow (RRID:SCR_000009) | software resource | Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05617 | SCR_000009 | ncdfFlow: A package that provides ncdf based storage for flow cytometry data | 2026-09-03 04:43:00 | 0 | ||||||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-03 04:43:07 | 0 | ||||||
|
flowBin Resource Report Resource Website |
flowBin (RRID:SCR_000051) | software resource | A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers. | software package, flow cytometry data, r, cell based assay, expression |
is related to: CRAN has parent organization: Bioconductor has parent organization: BC Cancer Agency |
Canadian Cancer Society ; International Society for the Advancement of Cytometry ; Michael Smith Foundation for Health Research ; NIBIB R01EB008400 |
PMID:25600947 | Free, Available for download, Freely available | OMICS_05593 | SCR_000051 | flowBin - Combining multitube flow cytometry data by binning | 2026-09-03 04:43:06 | 0 |
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