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 client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data.

This is a package with metadata for fast genotyping Affymetrix GenomeWideSnp_6 arrays using the crlmm package.

This package provides data needed to use the ITALICS package.

This package provides functions for performing print-run and array level quality assessment.

This package supports data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

This package adductomicsR processes data generated by the second stage of mass spectrometry (MS2) to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies level mass spectral peaks from first stage of mass spectrometry (MS1) data.

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 functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

This package models a RESTful service as if it were a nested R list.

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010; Costa et al. FEBS J, 288:2311-2331, 2021.

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).

EBarrays provides tools for the analysis of replicated/unreplicated microarray data.

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

This package provides basic features for the automated analysis of Affymetrix arrays.

This package provides a port of the matrixStats API for use with DelayedMatrix objects from the DelayedArray package. It contains high-performing functions operating on rows and columns of DelayedMatrix objects, e.g. colMedians, rowMedians, colRanks, rowRanks, colSds, and rowSds. Functions are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.

This package provides functions that are needed by many other packages on Bioconductor or which replace R functions.

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

This package contains functions and classes that are needed by arrayCGH packages.

This package provides example datasets that represent 'real world examples' of Affymetrix data, unlike the artificial examples included in the package affy.

This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

This package defines classes for "class discovery" in the OOMPA project. Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.