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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | ArrayTools - GeneChip Analysis Package | 2026-08-01 12:01:47 | 92 | ||||||
|
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 | affyPLM - Methods for fitting probe-level models | 2026-08-01 12:01:27 | 160 | |||||||
|
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 | Power Law Global Error Model | 2026-08-01 12:01:49 | 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 | Principal Variance Component Analysis | 2026-08-01 12:01:39 | 24 | |||||||
|
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 | metaArray - Integration of Microarray Data for Meta-analysis | 2026-08-01 12:01:39 | 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 | Significant Gene Expression Profile Differences in Time Course Microarray Data | 2026-08-01 12:01:49 | 222 | ||||||
|
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 | Harshlight - A corrective make-up program for microarray chips | 2026-08-01 12:01:48 | 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 | MiChip Parsing and Summarizing Functions | 2026-08-01 12:01:39 | 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 | fRMA - Frozen RMA and Barcode | 2026-08-01 12:01:28 | 74 | |||||
|
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 | Quality metrics on microarray data sets | 2026-08-01 12:01:48 | 180 | ||||||
|
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 | 2026-08-01 12:01:28 | 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 | 2026-08-01 12:01:28 | 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 | 2026-08-01 12:01:49 | 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 | 2026-08-01 12:01:28 | 64 | |||||||
|
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 | 2026-08-01 12:01:27 | 16 | |||||||
|
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 | 2026-08-01 12:01:27 | 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 | 2026-08-01 12:01:47 | 14 | |||||
|
ffpe Resource Report Resource Website 100+ 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 | 2026-08-01 12:01:38 | 496 | ||||||
|
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 | 2026-08-01 12:01:37 | 0 | ||||||
|
GenGIS Resource Report Resource Website 10+ mentions |
GenGIS (RRID:SCR_001465) | software resource | A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. It provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries. | standalone software | is listed by: OMICtools | Genome Atlantic ; Genome Canada ; Biomonitoring 2.0 Project ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Tula Foundation ; Natural Sciences and Engineering Research Council of Canada ; Dalhousie Faculty of Computer Science |
PMID:23922841 | Free, Available for download, Freely available | OMICS_04013 | http://kiwi.cs.dal.ca/GenGIS/ | SCR_001465 | 2026-08-01 12:01:30 | 38 |
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