The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This package hence can be used to group features, and its results can be used as an input for the QFeatures package which allows aggregating abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. xcms).

This package performs multiple co-inertia analysis of omics datasets.

This software ADAM is a Gene set enrichment analysis (GSEA) package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions. The corresponding roles are extracted from the default collections like Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG). ADAM show their significance by calculating the p-values referring to gene diversity and activity. Each group of genes is called Group of functionally associated genes (GFAG).

The mia package implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

The package ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be transformed into expression data matrix. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A graphical user interface (GUI) is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.

This package contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.

This package provides Affymetrix Human Genome U95 Set annotation data (hgu95av2) assembled using data from public data repositories.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

This package implements methods to remove unwanted variation (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

This is a representation of public golub data with some covariate data of provenance unknown to the maintainer at present; it now employs ExpressionSet format.

This package provides the complete genome sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top:

1. the mask of assembly gaps (AGAPS mask);

2. the mask of intra-contig ambiguities (AMB mask);

3. the mask of repeats from RepeatMasker (RM mask);

4. the mask of repeats from Tandem Repeats Finder (TRF mask).

Only the AGAPS and AMB masks are "active" by default. The sequences are stored in MaskedDNAString objects.

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.

DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It models the expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.

This package provides functions for reading array comparative genomic hybridization (aCGH) data from image analysis output files and clone information files, creation of aCGH objects for storing these data. Basic methods are accessing/replacing, subsetting, printing and plotting aCGH objects.

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

This package provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. It currently supports human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array.

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.

This package provides a set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison through each base position across the genome region of interest. The difference is inferred by Fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells. PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.

The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE.