This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome.

This package provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries.

Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet.

This package provides a roclet for roxygen2 that identifies and processes code blocks in your documentation marked with `@longtests`. These blocks should contain tests that take a long time to run and thus cannot be included in the regular test suite of the package. When you run `roxygen2::roxygenise` with the `longtests_roclet`, it will extract these long tests from your documentation and save them in a separate directory. This allows you to run these long tests separately from the rest of your tests, for example, on a continuous integration server that is set up to run long tests.

The barbieQ package provides a series of robust statistical tools for analysing barcode count data generated from cell clonal tracking (i.e., lineage tracing) experiments. In these experiments, an initial cell and its offspring collectively form a clone (i.e., lineage). A unique barcode sequence, incorporated into the DNA of the inital cell, is inherited within the clone. This one-to-one mapping of barcodes to clones enables clonal tracking of their behaviors. By counting barcodes, researchers can quantify the population abundance of individual clones under specific experimental perturbations. barbieQ supports barcode count data preprocessing, statistical testing, and visualization.

Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects.

Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv2) and available at the URGI (INRA).

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro2, 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), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

R interface for importing and analyzing enzyme information from the BRENDA database.

Full genome sequences for Arabidopsis thaliana as provided by TAIR (TAIR9 Genome Release) and stored in Biostrings objects. Note that TAIR10 is an "annotation release" based on the same genome assembly as TAIR9.

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects.

Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects.

the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.

Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.

Microarray analysis methods that use BufferedMatrix objects.

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects.

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau4, 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), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

Oryza sativa full genome as provided by MSU (MSU7 Genome Release) and stored in Biostrings objects.

Base annotation databases for bovine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

Extends beachmat to initialize tatami matrices from TileDB-backed arrays. This allows C++ code in downstream packages to directly call the TileDB C/C++ library to access array data, without the need for block processing via DelayedArray. Developers only need to import this package to automatically extend the capabilities of beachmat::initializeCpp to TileDBArray instances.

Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac3, 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), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.

Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam2, 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), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut2, Feb. 2013) and stored in Biostrings objects.