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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ArrayTools Resource Report Resource Website 50+ mentions |
ArrayTools (RRID:SCR_001313) | ArrayTools | software resource | Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases. | annotation, differential expression, microarray, one channel, preprocessing, quality control, report writing, statistical method, visualization, FASEB list |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02022 | http://www.bioconductor.org/packages/release/bioc/html/ArrayTools.html | SCR_001313 | SciCrunch Registry | ArrayTools - GeneChip Analysis Package | 2026-11-07 11:54:21 | 94 | ||||||
|
affyPLM Resource Report Resource Website 100+ mentions |
affyPLM (RRID:SCR_001319) | affyPLM | software resource | Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools. | microarray, one channel, preprocessing, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02017 | SCR_001319 | SciCrunch Registry | affyPLM - Methods for fitting probe-level models | 2026-11-07 11:54:16 | 163 | |||||||
|
plgem Resource Report Resource Website 10+ mentions |
plgem (RRID:SCR_001355) | plgem | software resource | Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets. | differential expression, microarray, proteomics, 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_01984, biotools:plgem | https://bio.tools/plgem | SCR_001355 | SciCrunch Registry | Power Law Global Error Model | 2026-11-07 11:54:29 | 16 | ||||||
|
PVCA Resource Report Resource Website 10+ mentions |
PVCA (RRID:SCR_001356) | PVCA | software resource | Software package that contains the function to assess the batch sourcs by fitting all sources as random effects including two-way interaction terms in the Mixed Model (depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book Batch Effects and Noise in Microarray Experiements, chapter 12. | microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01983 | SCR_001356 | SciCrunch Registry | Principal Variance Component Analysis | 2026-11-07 11:54:23 | 25 | |||||||
|
metaArray Resource Report Resource Website |
metaArray (RRID:SCR_001353) | metaArray | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) and combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform. | differential expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17900369 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01986 | SCR_001353 | SciCrunch Registry | metaArray - Integration of Microarray Data for Meta-analysis | 2026-11-07 11:54:17 | 0 | ||||||
|
maSigPro Resource Report Resource Website 100+ mentions |
maSigPro (RRID:SCR_001349) | maSigPro | software resource | A regression based software package to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments. | differential expression, gene expression, time course, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16481333 | Free, Available for download, Freely available | OMICS_01990 | SCR_001349 | SciCrunch Registry | Significant Gene Expression Profile Differences in Time Course Microarray Data | 2026-11-07 11:54:16 | 236 | ||||||
|
genArise Resource Report Resource Website 10+ mentions |
genArise (RRID:SCR_001346) | genArise | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | genArise - Microarray Analysis tool | 2026-11-07 11:54:28 | 24 | |||||||
|
Harshlight Resource Report Resource Website 1+ mentions |
Harshlight (RRID:SCR_001340) | Harshlight | software resource | Software package used to detect extended, diffuse and compact blemishes on microarray chips. It automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. | microarray, preprocessing, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16336691 | Free, Available for download, Freely available | OMICS_02001 | SCR_001340 | SciCrunch Registry | Harshlight - A corrective make-up program for microarray chips | 2026-11-07 11:54:22 | 6 | ||||||
|
MiChip Resource Report Resource Website 1+ mentions |
MiChip (RRID:SCR_001341) | MiChip | software resource | Software package that takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages. | microarray, preprocessing, mirna, hybridization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16540696 PMID:18274534 |
Free, Available for download, Freely available | OMICS_02000 | SCR_001341 | SciCrunch Registry | MiChip Parsing and Summarizing Functions | 2026-11-07 11:54:16 | 7 | ||||||
|
fRMA Resource Report Resource Website 50+ mentions |
fRMA (RRID:SCR_001345) | fRMA | software resource | Preprocessing and analysis software for single microarrays and microarray batches. | microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23044545 | Free, Available for download, Freely available | biotools:frma, OMICS_01994 | https://bio.tools/frma | SCR_001345 | SciCrunch Registry | fRMA - Frozen RMA and Barcode | 2026-11-07 11:54:16 | 76 | |||||
|
arrayQualityMetrics Resource Report Resource Website 100+ mentions |
arrayQualityMetrics (RRID:SCR_001335) | arrayQualityMetrics | software resource | Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported. | microarray, quality control, report writing |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
PMID:19106121 | Free, Available for download, Freely available | OMICS_02005 | SCR_001335 | SciCrunch Registry | Quality metrics on microarray data sets | 2026-11-07 11:54:16 | 183 | ||||||
|
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 | SciCrunch Registry | Differential Expression via Distance Summary, Differential Expression via Distance Summary for Microarray Data | 2026-11-07 11:54:29 | 15 | ||||||
|
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 | SciCrunch Registry | 2026-11-07 11:53:54 | 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 | SciCrunch Registry | 2026-11-07 11:53:52 | 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 | SciCrunch Registry | VariantAnnotation - Annotation of Genetic Variants | 2026-11-07 11:53:52 | 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 | SciCrunch Registry | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-11-07 11:53:53 | 5 | ||||||
|
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 | SciCrunch Registry | CorMut - Detect the correlated mutations based on selection pressure | 2026-11-07 11:53:51 | 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 | SciCrunch Registry | flowBin - Combining multitube flow cytometry data by binning | 2026-11-07 11:53:52 | 0 | ||||||
|
metaSeq Resource Report Resource Website |
metaSeq (RRID:SCR_000056) | metaSeq | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 11:53:52 | 0 | ||||||||
|
cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | data analysis software, data processing software, software application, software resource, 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 | SciCrunch Registry | cn.farms - factor analysis for copy number estimation | 2026-11-07 11:53:58 | 0 |
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