ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction(ANCOM-BC) and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package were designed to correct these biases and construct statistically consistent estimators.

The affyILM package is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behal of the Langmuir model.

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

This package provides a quality control pipeline for ChIP-exo/nexus sequencing data.

This package provides a dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessibility for new Bioconductor users is hopefully increased.

This package provides processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages.

This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).

This is a package for biclustering analysis and exploration of results.

This is a package with metadata for genotyping Illumina 370k arrays using the crlmm package.

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

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

This package provides a pipeline for analysing Capture Hi-C data.

This package can do differential expression analysis of RNA-seq expression profiles with biological replication. It implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. It be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

This is an annotation package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

This package provides gene-level read counts from RNA-Seq for gallein-treated and control zebrafish.

This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display copy number variation. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.

This package provides the headers and static library of Protocol buffers for other R packages to compile and link against.

This package provides a package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. This package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.

This package implements some simple capabilities for representing and manipulating hypergraphs.

This package provides routines for parsing Affymetrix data files based upon file format information. The primary focus is on accessing the CEL and CDF file formats.

Read bigWig and bigBed files using libBigWig. This package provides lightweight access to the binary bigWig and bigBed formats developed by the UCSC Genome Browser group.

This is an R package to make it easier to import and store phylogenetic trees with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic trees with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

DSS is an R library performing differential analysis for count-based sequencing data. It detects differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.