The purpose of biocViews is to create HTML pages that categorize packages in a Bioconductor package repository according to keywords, also known as views, in a controlled vocabulary.

CopywriteR extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

This package can be used to test two sets of gene lists and visualize the results.

This package implements the gene expression anti-profiles method. Anti-profiles are a new approach for developing cancer genomic signatures that specifically take advantage of gene expression heterogeneity. They explicitly model increased gene expression variability in cancer to define robust and reproducible gene expression signatures capable of accurately distinguishing tumor samples from healthy controls.

This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

This package provides high performance functions for row and column operations on sparse matrices. Currently, the optimizations are limited to data in the column sparse format.

This package implements a method to rapidly assess cell type identity using both functional and random gene sets and it allows users to quantify cell type replicability across datasets using neighbor voting. MetaNeighbor works on the basis that cells of the same type should have more similar gene expression profiles than cells of different types.

This package provides data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array.

ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. The ATACseqQC package was developed to help users to quickly assess whether their ATAC-seq experiment is successful. It includes diagnostic plots of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.

This package provides a collection of software tools for calculating distance measures.

tRNAdbImport imports the entries of the tRNAdb and mtRNAdb as GRanges object.

This package uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers. For this it uses segmented data from the QDNAseq package, which in turn uses a number of dependencies to turn mapped reads into segmented data. ACE will run QDNAseq or use its output rds-file of segmented data. It will subsequently run through all samples in the object(s), for which it will create individual subdirectories. For each sample, it will calculate how well the segments fit (the relative error) to integer copy numbers for each percentage of tumor cells (cells with divergent segments).

BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

This package 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.

This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

The MassSpecWavelet package aims to process Mass Spectrometry (MS) data mainly through the use of wavelet transforms. It supports peak detection based on Continuous Wavelet Transform (CWT).

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.

This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article 'Conservation of an RNA regulatory map between Drosophila and mammals' by Brooks et al., Genome Research 2011.

This package exposes an annotation database generated from Ensembl.

EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.

This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.