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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ITALICS Resource Report Resource Website |
ITALICS (RRID:SCR_001274) | ITALICS | software resource | Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set. | affymetrix, copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18252739 | Free, Available for download, Freely available | OMICS_02064 | SCR_001274 | 2026-02-14 01:59:59 | 0 | |||||||
|
GenoSet Resource Report Resource Website |
GenoSet (RRID:SCR_001275) | GenoSet | data analysis software, software resource, data processing software, software application | Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. | copy number variation, data representation, infrastructure, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License, v2 | OMICS_02063 | SCR_001275 | genoset - Provides classes similar to ExpressionSet for copy number analysis | 2026-02-14 01:59:57 | 0 | |||||||
|
mBPCR Resource Report Resource Website |
mBPCR (RRID:SCR_001273) | mBPCR | software resource | Software package that estimates the DNA copy number profile to detect regions with copy number changes. | copy number variation, microarray, snp, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02065 | SCR_001273 | mBPCR - Bayesian Piecewise Constant Regression for DNA copy number estimation | 2026-02-14 02:00:04 | 0 | |||||||
|
CGHregions Resource Report Resource Website 1+ mentions |
CGHregions (RRID:SCR_001278) | CGHregions | software resource | Software package for dimension Reduction for Array CGH Data with Minimal Information Loss. | copy number variation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19455235 | Free, Available for download, Freely available | OMICS_02058 | SCR_001278 | CGHregions - Dimension Reduction for Array CGH Data with Minimal Information Loss | 2026-02-14 02:00:04 | 4 | ||||||
|
CGHbase Resource Report Resource Website 1+ mentions |
CGHbase (RRID:SCR_001279) | CGHbase | data analysis software, software resource, data processing software, software application | Software package that contains functions and classes that are needed by arrayCGH packages. | copy number variation, infrastructure, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02057 | SCR_001279 | CGHbase: Base functions and classes for arrayCGH data analysis | 2026-02-14 01:59:59 | 1 | |||||||
|
quantsmooth Resource Report Resource Website 1+ mentions |
quantsmooth (RRID:SCR_001271) | quantsmooth | software resource | Software package for quantile smoothing and genomic visualization of array data. | copy number variation, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:15572474 | Free, Available for download, Freely available | OMICS_02067, BioTools:quantsmooth, biotools:quantsmooth | https://bio.tools/quantsmooth https://bio.tools/quantsmooth https://bio.tools/quantsmooth |
SCR_001271 | 2026-02-14 01:59:57 | 1 | ||||||
|
SNPchip Resource Report Resource Website 10+ mentions |
SNPchip (RRID:SCR_001269) | SNPchip | software resource | Software package that contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor, including the R packages Biobase and oligo. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality. | dna copy number, snp, genetic variability, visualization, high throughput, snp chip, microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:17204461 | Free, Available for download, Freely available | OMICS_02069, biotools:snpchip | https://bio.tools/snpchip | SCR_001269 | 2026-02-14 02:00:04 | 13 | ||||||
|
VegaMC Resource Report Resource Website 1+ mentions |
VegaMC (RRID:SCR_001267) | VegaMC | software resource | Software package that enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, it produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported. | copy number variation, acgh, chromosomal imbalance |
is listed by: OMICtools is related to: PennCNV has parent organization: Bioconductor |
Cancer | PMID:22815357 | Free, Available for download, Freely available | OMICS_02071 | SCR_001267 | VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer | 2026-02-14 01:59:57 | 1 | |||||
|
VanillaICE Resource Report Resource Website 1+ mentions |
VanillaICE (RRID:SCR_001268) | VanillaICE | software resource | Software package using Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays. | statistics, dna copy number, snp, genetic variability, visualization, high throughput, snp chip, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:19609370 | GNU General Public License, v2 or newer | OMICS_02070 | http://www.biostat.jhsph.edu/~rscharpf/software/index.html | SCR_001268 | vanilla-ice | 2026-02-14 01:59:59 | 3 | |||||
|
sRAP Resource Report Resource Website 10+ mentions |
sRAP (RRID:SCR_001297) | sRAP | software resource | Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data. | gene expression, differential expression, go, gene set enrichment, microarray, preprocessing, quality control, rna-seq, statistical method, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02038 | http://www.bioconductor.org/packages/release/bioc/html/sRAP.html | SCR_001297 | Simplified RNA-Seq Analysis | 2026-02-14 02:00:05 | 15 | ||||||
|
SCAN.UPC Resource Report Resource Website 10+ mentions |
SCAN.UPC (RRID:SCR_001334) | SCAN.UPC | software resource | A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A | microarray, one channel, preprocessing, rna-seq, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02006 | SCR_001334 | Single-channel array normalization (SCAN) and Universal exPression Codes (UPC), Single-channel array normalization and Universal exPression Codes | 2026-02-14 01:59:59 | 11 | |||||||
|
SNM Resource Report Resource Website 1+ mentions |
SNM (RRID:SCR_001299) | SNM | software resource | Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest. | differential expression, exon array, gene expression, microarray, multi channel, multiple comparison, one channel, preprocessing, quality control, transcription, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02036 | SCR_001299 | Supervised Normalization of Microarrays | 2026-02-14 01:59:58 | 1 | |||||||
|
betr Resource Report Resource Website 10+ mentions |
betr (RRID:SCR_001332) | betr | software resource | Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data. | differentially expression, gene, microarray, time-course |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20003283 | Free, Available for download, Freely available | OMICS_01997 | http://www.bioconductor.org/packages/release/bioc/html/betr.html | SCR_001332 | Bayesian Estimation of Temporal Regulation | 2026-02-14 02:00:06 | 17 | |||||
|
gprege Resource Report Resource Website 1+ mentions |
gprege (RRID:SCR_001324) | gprege | software resource | Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007). | differential expression, microarray, preprocessing, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:21599902 | Free, Available for download, Freely available | OMICS_02011, biotools:gprege | http://www.bioconductor.org/packages/release/bioc/html/gprege.html | SCR_001324 | Gaussian Process Ranking and Estimation of Gene Expression time-series | 2026-02-14 02:00:06 | 1 | |||||
|
waveTiling Resource Report Resource Website |
waveTiling (RRID:SCR_001322) | waveTiling | software resource | Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models. | differential expression, microarray, gene expression, time course |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22974078 | Free, Available for download, Freely available | OMICS_02014 | http://www.bioconductor.org/packages/release/bioc/html/waveTiling.html | SCR_001322 | waveTiling - Wavelet-Based Models for Tiling Array Transcriptome Analysis | 2026-02-14 01:59:58 | 0 | |||||
|
AffyExpress Resource Report Resource Website 1+ mentions |
AffyExpress (RRID:SCR_001321) | AffyExpress | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. | differential expression, microarray, annotation, one channel, preprocessing, quality control, report writing, visualization, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02015 | SCR_001321 | AffyExpress - Affymetrix Quality Assessment and Analysis Tool | 2026-02-14 02:00:00 | 2 | |||||||
|
beadarray Resource Report Resource Website 100+ mentions |
beadarray (RRID:SCR_001314) | beadarray | software resource | Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. | microarray, quality control, one channel, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
PMID:17586828 | GNU General Public License, v2 | OMICS_02021, biotools:beadarray | https://bio.tools/beadarray | SCR_001314 | beadarray - Quality assessment and low-level analysis for Illumina BeadArray data | 2026-02-14 02:00:00 | 119 | |||||
|
arrayMvout Resource Report Resource Website 1+ mentions |
arrayMvout (RRID:SCR_001317) | arrayMvout | software resource | Software package that supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate. | infrastructure, microarray, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02019 | SCR_001317 | arrayMvout - Multivariate outlier detection for expression array QA | 2026-02-14 02:00:00 | 1 | |||||||
|
affyQCReport Resource Report Resource Website 10+ mentions |
affyQCReport (RRID:SCR_001318) | affyQCReport | software resource | Software package to create a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. | microarray, one channel, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02018 | http://www.bioconductor.org/packages/release/bioc/html/affyQCReport.html | SCR_001318 | affyQCReport - QC Report Generation for affyBatch objects | 2026-02-14 01:59:58 | 44 | ||||||
|
maigesPack Resource Report Resource Website |
maigesPack (RRID:SCR_001351) | maigesPack | software resource | Software package that uses functions to handle and analyze cDNA microarray data. | classification, clustering, differential expression, graph, network, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01988 | http://www.bioconductor.org/packages/release/bioc/html/maigesPack.html | SCR_001351 | 2026-02-14 02:00:01 | 0 |
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