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Platform Design Info for Affymetrix Cytogenetics_Array.
Platform Design Info for Affymetrix miRNA-4_0.
Platform Design Info for The Manufacturer's Name Medicago.
Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter.
PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.
CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.
Platform Design Info for Affymetrix MoGene-1_0-st-v1.
Platform Design Info for Affymetrix MTA-1_0.
Platform Design Info for Affymetrix Clariom_D_Human.
Platform Design Info for The Manufacturer's Name HG_U95E.
Platform Design Info for Affymetrix EquGene-1_0-st.
This package provides a package containing an environment representing the Plasmodium_Anopheles.cdf file.
This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.
This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.
Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.
Platform Design Info for Affymetrix CHOGene-2_1-st.
Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package.
Platform Design Info for NimbleGen feinberg_hg18_me_hx1.
This package provides a DelayedArray interface for plink bed files. There is support for interfacing to plink genotype data via RangedSummarizedExperiment. Example data from the GEUVADIS project (internationalgenome.org) are used for demonstration.
Platform Design Info for Affymetrix RabGene-1_0-st.
Platform Design Info for Affymetrix miRNA-2_0.
Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.
This package provides a Bioconductor data package for the Varambally dataset.
Platform Design Info for The Manufacturer's Name Drosophila_2.