rtracklayer is an extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

This package is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. r-fourcseq provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a Python script to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.

BgeeCall allows generating present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee.

This package provides platform design info for Affymetrix Mapping50K_Hind240.

This package offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

This package contains functions for exploratory oligonucleotide array analysis.

TreeSummarizedExperiment extends SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.

This package provides flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.

This package provides tools to parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data.

This package contains classes used in model-view-controller (MVC) design.

This package facilitates phyloseq exploration and analysis of taxonomic profiling data. This package provides tools for the manipulation, statistical analysis, and visualization of taxonomic profiling data. In addition to targeted case-control studies, microbiome facilitates scalable exploration of population cohorts. This package supports the independent phyloseq data format and expands the available toolkit in order to facilitate the standardization of the analyses and the development of best practices.

R-escape streamlines gene set enrichment analysis for single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize GSEA across individual cells.

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

Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The package contains functions for combining the results of multiple runs of gene set analyses.

This is a package that can be used for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

This package provides a database of PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137.

The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.

Quickly find motif matches for many motifs and many sequences. This package wraps C++ code from the MOODS motif calling library.

This package provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

This package was derived from Rsymphony. The package provides an R interface to SYMPHONY, a linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code, while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY.

This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).

Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. decoupleR is a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

This package provides infrastructure shared by all Biostrings-based genome data packages and support for efficient SNP representation.