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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CYCLE Resource Report Resource Website 1+ mentions |
CYCLE (RRID:SCR_001328) | CYCLE | software resource | Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models. | r, microarray, time course, periodic expression pattern, time-series, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18310054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02010, biotools:cycle | http://www.bioconductor.org/packages/release/bioc/html/cycle.html, https://bio.tools/cycle | SCR_001328 | 2026-09-19 12:49:39 | 4 | ||||||
|
LMGene Resource Report Resource Website 1+ mentions |
LMGene (RRID:SCR_001329) | LMGene | software resource | Software package for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays. | differential expression, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02009 | http://www.bioconductor.org/packages/release/bioc/html/LMGene.html | SCR_001329 | 2026-09-19 12:49:39 | 4 | |||||||
|
affylmGUI Resource Report Resource Website 10+ mentions |
affylmGUI (RRID:SCR_001320) | affylmGUI | software resource | R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11. | affymetrix, differential expression, r, data import, differential expression, gui, microarray, multiple comparison, one channel, preprocessing, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia has parent organization: Bioconductor |
PMID:16455752 | Free, Available for download, Freely available | biotools:affylmgui, OMICS_02016 | http://www.bioconductor.org/packages/release/bioc/html/affylmGUI.html, https://bio.tools/affylmgui | SCR_001320 | Affymetrix linear modeling Graphical User Interface | 2026-09-19 12:49:39 | 31 | |||||
|
arrayQuality Resource Report Resource Website 1+ mentions |
arrayQuality (RRID:SCR_001315) | arrayQuality | software resource | Software functions for performing print-run and array level quality assessment. | microarray, quality control, two channel, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU Lesser General Public License | OMICS_02020 | SCR_001315 | arrayQuality - Assessing array quality on spotted arrays | 2026-09-19 12:49:38 | 8 | |||||||
|
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 | 2026-09-19 12:49:38 | 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 | affyPLM - Methods for fitting probe-level models | 2026-09-19 12:49:40 | 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 | Power Law Global Error Model | 2026-09-19 12:49:39 | 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 | 2026-09-19 12:49:40 | 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 | metaArray - Integration of Microarray Data for Meta-analysis | 2026-09-19 12:49:39 | 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 | 2026-09-19 12:49:39 | 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 | genArise - Microarray Analysis tool | 2026-09-19 12:49:39 | 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 | Harshlight - A corrective make-up program for microarray chips | 2026-09-19 12:49:39 | 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 | 2026-09-19 12:49:39 | 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 | 2026-09-19 12:49:40 | 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 | Quality metrics on microarray data sets | 2026-09-19 12:49:39 | 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 | Differential Expression via Distance Summary, Differential Expression via Distance Summary for Microarray Data | 2026-09-19 12:49:40 | 15 | ||||||
|
DDBJ Sequence Read Archive Resource Report Resource Website 50+ mentions |
DDBJ Sequence Read Archive (RRID:SCR_001370) | DRA | data or information resource, data repository, database, service resource, storage service resource | Archive database for output data generated by next-generation sequencing machines including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA). Please submit the trace data from conventional capillary sequencers to DDBJ Trace Archive., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, next-generation sequencing, sequence read, FASEB list |
is listed by: OMICtools is affiliated with: INSDC is related to: NCBI Sequence Read Archive (SRA) is related to: European Nucleotide Archive (ENA) is related to: NCBI Sequence Read Archive (SRA) has parent organization: DNA DataBank of Japan (DDBJ) |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:22009675 PMID:21062823 |
THIS RESOURCE IS NO LONGER IN SERVICE | r3d100013696, OMICS_01027, nlx_152515 | http://trace.ddbj.nig.ac.jp/dra/ | SCR_001370 | 2026-09-19 12:49:40 | 95 | |||||
|
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 | 2026-09-19 12:49:40 | 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 | 2026-09-19 12:49:40 | 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 | 2026-09-19 12:49:41 | 66 |
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