This package exposes an annotation database generated from Ensembl.

This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data.

This package provides various wrapper functions that have been written to streamline the more common analyses that a Biostatistician might see.

This package provides a database of SIFT predictions for Homo sapiens dbSNP build 132.

This package provides dataset samples (Affymetrix: Expression, Gene, Exon, SNP; NimbleGen: Expression, Tiling) to be used with the oligo package.

This package is designed to store minor allele frequency data. It retrieves this data from the Genome Aggregation Database (gnomAD version 3.1.2) for the human genome version GRCh38.

This is a package for Differential Expression Analysis of RNA-seq data. It features a variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with repeated or longitudinal data.

This package provides tools for exporting and importing classification trees and clusters to other programs.

This package provides tools for alignment, quantification and analysis of second and third generation sequencing data. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.

This package manages the installation of CMake for building Bioconductor packages. This avoids the need for end-users to manually install CMake on their system. No action is performed if a suitable version of CMake is already available.

This package provides a set of functions to create and interact with dynamic documents and vignettes.

This package provides Ion Trap positive ionization mode data in mzML file format. It includes a subset from 500-850 m/z and 1190-1310 seconds, including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5; LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example files for various search engines.

This package provides the full genome sequences for Bos taurus (UCSC version bosTau8).

This is a package providing tools to quantify and interpret multiple sources of biological and technical variation in gene expression experiments. It uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. The package includes dream differential expression analysis for repeated measures.

This package provides classes and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters are used by ensembldb, Organism.dplyr, and other packages.

The parody package provides routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

This package provides functions and classes for de novo prediction of transcription factor binding consensus by heuristic search.

This R package is for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis, such as differential gene expression or transcript usage.

Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.

This package provides memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

This package provides Affymetrix HG_U95A Array annotation data (chip hgu95a) assembled using data from public repositories.

The fishpond package contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.

This is the core package for the automated analysis of Affymetrix arrays.

This package provides C and C++ HDF5 libraries for use in R packages.