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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-14 02:00:02 | 222 | ||||||
|
genArise Resource Report Resource Website 10+ mentions |
genArise (RRID:SCR_001346) | genArise | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:00:07 | 22 | |||||||
|
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 | 2026-02-14 01:59:59 | 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 | 2026-02-14 02:00:01 | 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 | 2026-02-14 02:00:01 | 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 | 2026-02-14 02:00:01 | 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 | 2026-02-14 02:00:01 | 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 | 2026-02-14 01:59:59 | 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 | 2026-02-14 02:00:07 | 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 | 2026-02-14 02:00:02 | 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 | 2026-02-14 02:00:00 | 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 | 2026-02-14 01:59:58 | 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 | 2026-02-14 02:00:05 | 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 | 2026-02-14 02:00:00 | 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 | 2026-02-14 02:00:00 | 0 | ||||||
|
CNTools Resource Report Resource Website |
CNTools (RRID:SCR_000281) | CNTools | software resource | Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data. | copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02061 | SCR_000281 | CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses | 2026-02-14 01:59:40 | 0 | |||||||
|
TransView Resource Report Resource Website |
TransView (RRID:SCR_000358) | TransView | software resource | Software package to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq. | rna-seq, chip-seq, clustering, dna methylation, data import, gene expression, methyl-seq, microarray, multiple comparison, sequencing, transcription, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02048 | SCR_000358 | 2026-02-14 01:59:42 | 0 | ||||||||
|
pvac Resource Report Resource Website |
pvac (RRID:SCR_000359) | pvac | software resource | Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC). | microarray, one channel, quality control, affymetrix, principal component analysis, 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:pvac, OMICS_02031 | https://bio.tools/pvac | SCR_000359 | pvac: PCA-based gene filtering for Affymetrix arrays | 2026-02-14 01:59:41 | 0 | ||||||
|
flowFlowJo Resource Report Resource Website 10+ mentions |
flowFlowJo (RRID:SCR_000410) | software resource | A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956421 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05598 | SCR_000410 | flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm | 2026-02-14 01:59:43 | 21 | |||||||
|
cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | data processing software, data analysis software, software toolkit, software application, software resource | 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 | 2026-02-14 01:59:42 | 0 |
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