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.

This package is importing data from Illumina SNP experiments and it performs copy number calculations and reports.

SGSeq is a package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.

This package provides functions for plotting genomic data.

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans.

This package provides an array-like container for convenient access and manipulation of HDF5 datasets. It supports delayed operations and block processing.

This package implements some simple graph handling capabilities for R.

This package enables you to read and manipulate genome intervals and signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

This package r-chromvar determines variation in chromatin accessibility across sets of annotations or peaks. r-chromvar is designed primarily for single-cell or sparse chromatin accessibility data like single cell assay for transposase-accessible chromatin using sequencing (scATAC-seq or sparse bulk ATAC or deoxyribonuclease sequence (DNAse-seq) experiments.

This package provides supporting data for the TCGAbiolinksGUI package.

This package provides UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species.

This package provides the core data structure and API to represent and interact with gated cytometry data.

This package provides a function to impute missing gene expression microarray data, using nearest neighbor averaging.

This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

This package implements tools for delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. It also supports partial computation of residuals where selected factors are to be preserved in the output matrix. It implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.

This package provides tools for estimating variance-mean dependence in count data from high-throughput genetic sequencing assays and for testing for differential expression based on a model using the negative binomial distribution.

This package implements functions for copy number variant calling, plotting, export and analysis from whole-genome single cell sequencing data.

This package interfaces R with the graphviz library for plotting R graph objects from the graph package.

This is a data package for JASPAR 2016. To search this databases, please use the package TFBSTools.

mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.

ggtreeExtra extends the method for mapping and visualizing associated data on phylogenetic tree using ggtree. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by ggtree with the grammar of ggplot2.