Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3, 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.

This package provides a client for BEDbase. bedbaser provides access to the API at api.bedbase.org. It also includes convenience functions to import BED files into GRanges objects and BEDsets into GRangesLists.

Microarray analysis methods that use BufferedMatrix objects.

Full genomic sequences for UCSC genome hs1 (the hs1 genome is based on assembly T2T-CHM13v2.0, with GenBank assembly accession GCA_009914755.4). The sequences are stored in DNAString objects.

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.

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.

The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects.

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau3, 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 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.

This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects.

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn6, Jul. 2014) and stored in Biostrings objects.

Package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm described in the paper by J. Claesen, P. Dittwald, T. Burzykowski and D. Valkenborg.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bovine\_probe\_tab.

bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).

An small dataset that can be used to run examples from the beadarray vignette and examples.

Full genome sequences for Bos taurus (Cow) as provided by UCSC (genome bosTau9) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau9, 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 Apis mellifera as provided by NCBI (assembly Amel_HAv3.1, assembly accession GCF_003254395.2) and stored in Biostrings objects.

This package is built to perform GWAS analysis for non-Gaussian data using BG2. The BG2 method uses penalized quasi-likelihood along with nonlocal priors in a two step manner to identify SNPs in GWAS analysis. The research related to this package was supported in part by National Science Foundation awards DMS 1853549 and DMS 2054173.

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

Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac8, Nov. 2015) and stored in Biostrings objects.