This is a manifest package for Illumina's EPIC methylation arrays.

This package provides more than 2000 annotated position frequency matrices from nine public sources, for multiple organisms.

CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the "query space" or "reference space", and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.

This package provides S4 generic functions modeled after the matrixStats API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.

CelliD is a clustering-free method for extracting per-cell gene signatures from scRNA-seq. CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. The package can also be used to explore functional pathways enrichment in single cell data.

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.

The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.

This package helps with the analysis of array CGH data by detecting of the breakpoints in the genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

This package provides full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer10, Sep. 2014) and stored in Biostrings objects.

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

The atSNP package performs affinity tests of motif matches with the SNP (single nucleotide polymorphism) or the reference genomes and SNP-led changes in motif matches.

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

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

This package provides visualization tools for flow cytometry data.

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.

This package provides the data for the gene expression enrichment analysis conducted in the package ABAEnrichment. The package includes three datasets which are derived from the Allen Brain Atlas:

1. Gene expression data from Human Brain (adults) averaged across donors,

2. Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors, and

3. a developmental effect score based on the Developing Human Brain expression data.

All datasets are restricted to protein coding genes.

This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. It also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

This is a package for the analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

This package discovers differential features in hetero- and homogeneous omic data by a two-step method including subsampling LIMMA and NSCA. DECO reveals feature associations to hidden subclasses not exclusively related to higher deregulation levels.

This package provides a collection of tools for performing category analysis.

This package wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.

This package provides a set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

This package provides an annotation database of Mouse genome data. It is derived from the UCSC mm9 genome and based on the "knownGene" track. The database is exposed as a TxDb object.