Showing 17 of total 17 results (show query)
bioc
oligo:Preprocessing tools for oligonucleotide arrays
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
Maintained by Benilton Carvalho. Last updated 24 days ago.
microarrayonechanneltwochannelpreprocessingsnpdifferentialexpressionexonarraygeneexpressiondataimportzlib
3 stars 10.42 score 528 scripts 10 dependentsbioc
affycoretools:Functions useful for those doing repetitive analyses with Affymetrix GeneChips
Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.
Maintained by James W. MacDonald. Last updated 5 months ago.
reportwritingmicroarrayonechannelgeneexpression
6.07 score 117 scriptsbioc
ArrayExpress:Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet.
Maintained by Jose Marugan. Last updated 25 days ago.
microarraydataimportonechanneltwochannel
6.05 score 124 scripts 1 dependentsbioc
VanillaICE:A Hidden Markov Model for high throughput genotyping arrays
Hidden Markov Models for characterizing chromosomal alteration in high throughput SNP arrays.
Maintained by Robert Scharpf. Last updated 5 months ago.
5.36 score 63 scripts 1 dependentsbioc
crlmm:Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.
Maintained by Benilton S Carvalho. Last updated 28 days ago.
microarraypreprocessingsnpcopynumbervariation
4.78 score 37 scripts 3 dependentsbioc
frma:Frozen RMA and Barcode
Preprocessing and analysis for single microarrays and microarray batches.
Maintained by Matthew N. McCall. Last updated 5 months ago.
softwaremicroarraypreprocessing
4.72 score 87 scripts 1 dependentsbioc
puma:Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.
Maintained by Xuejun Liu. Last updated 11 days ago.
microarrayonechannelpreprocessingdifferentialexpressionclusteringexonarraygeneexpressionmrnamicroarraychiponchipalternativesplicingdifferentialsplicingbayesiantwochanneldataimporthta2.0
4.71 score 17 scriptsbioc
pdInfoBuilder:Platform Design Information Package Builder
Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.
Maintained by Benilton Carvalho. Last updated 5 months ago.
4.49 score 13 scriptsbioc
MAGAR:MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.
Maintained by Michael Scherer. Last updated 5 months ago.
regressionepigeneticsdnamethylationsnpgeneticvariabilitymethylationarraymicroarraycpgislandmethylseqsequencingmrnamicroarraypreprocessingcopynumbervariationtwochannelimmunooncologydifferentialmethylationbatcheffectqualitycontroldataimportnetworkclusteringgraphandnetwork
4.30 score 3 scriptsbioc
ITALICS:ITALICS
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
Maintained by Guillem Rigaill. Last updated 5 months ago.
4.08 scorebioc
mBPCR:Bayesian Piecewise Constant Regression for DNA copy number estimation
It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.
Maintained by P.M.V. Rancoita. Last updated 5 months ago.
acghsnpmicroarraycopynumbervariation
3.90 score 1 scriptsbioc
ChIPXpress:ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.
Maintained by George Wu. Last updated 5 months ago.
3.78 score 2 scriptsbioc
mimager:mimager: The Microarray Imager
Easily visualize and inspect microarrays for spatial artifacts.
Maintained by Aaron Wolen. Last updated 5 months ago.
infrastructurevisualizationmicroarraybioconductorbioinformatics
3.70 score 3 scriptsbioc
MinimumDistance:A Package for De Novo CNV Detection in Case-Parent Trios
Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.
Maintained by Robert Scharpf. Last updated 5 months ago.
microarraysnpcopynumbervariation
3.60 score 10 scriptsbioc
SCAN.UPC:Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
SCAN is a microarray normalization method to facilitate personalized-medicine workflows. 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 Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. 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.
Maintained by Stephen R. Piccolo. Last updated 5 months ago.
immunooncologysoftwaremicroarraypreprocessingrnaseqtwochannelonechannel
3.48 score 15 scriptsbioc
cn.farms:cn.FARMS - factor analysis for copy number estimation
This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.
Maintained by Andreas Mitterecker. Last updated 5 months ago.
microarraycopynumbervariationcpp
3.30 score 7 scriptsbioc
DrugVsDisease:Comparison of disease and drug profiles using Gene set Enrichment Analysis
This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.
Maintained by j. Saez-Rodriguez. Last updated 5 months ago.
microarraygeneexpressionclustering
3.30 score 8 scripts