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

Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.

This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies.

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

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

This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.

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.

This package provides fast maximum-likelihood phylogeny inference from noisy single-cell data using the ScisTree algorithm proposed by doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019). It makes the method applicable to massive single-cell datasets (>10,000 cells).

This package annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided.

Fastseg implements a very fast and efficient segmentation algorithm. It can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.

This package represents an integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. ActivePathways uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.

This package is an implementation of the Adaptively Weighted Fisher's method, including fast p-value computing, variability index, and meta-pattern.

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects.

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

This package provides Affymetrix HG-U133_Plus_2 array annotation data (chip hgu133plus2) assembled using data from public repositories.

This package provides tools for normalizing and analyzing of GeneChip Mapping 100K and 500K Set. Affymetrix GeneChip Human Mapping 100K and 500K Set allows the DNA copy number mea- surement of respectively 2× 50K and 2× 250K SNPs along the genome. Their high density allows a precise localization of genomic alterations and makes them a powerful tool for cancer and copy number polymorphism study.

The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides:

1. low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and

2. a framework that facilitates block processing of array-like objects (typically on-disk objects).

Gcrma adjusts for background intensities in Affymetrix array data which include optical noise and non-specific binding (NSB). The main function gcrma converts background adjusted probe intensities to expression measures using the same normalization and summarization methods as a Robust Multiarray Average (RMA). Gcrma uses probe sequence information to estimate probe affinity to NSB. The sequence information is summarized in a more complex way than the simple GC content. Instead, the base types (A, T, G or C) at each position along the probe determine the affinity of each probe. The parameters of the position-specific base contributions to the probe affinity is estimated in an NSB experiment in which only NSB but no gene-specific binding is expected.

This package provides Affymetrix HG-U133A Array annotation data (chip hgu133a) assembled using data from public repositories.

This package is a collection of gene expression data from a breast cancer study published in Wang et al. 2005 and Minn et al 2007.

This package provides tools to create and plot diffusion maps.

This package provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. It also provides some helper functions to assist development of other packages.

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

This package provides a set of protein ID mappings for PFAM, assembled using data from public repositories.