Full genome sequences for Mus musculus (Mouse) as provided by UCSC (genome mm10, based on GRCm38.p6) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm10, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask).

Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects.

This package provides a package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.

Affymetrix Affymetrix Bovine Array annotation data (chip bovine) assembled using data from public repositories.

This package provides tools to normalize (several) Hi-C data from replicates.

Full genome sequences for Mustela putorius furo (Ferret) as provided by UCSC (musFur1, Apr. 2011) and stored in Biostrings objects.

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg17, 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.

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

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.

The biodbChebi library provides access to the ChEBI Database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name, mass or other fields.

Full genome sequences for Chlamydomonas reinhardtii (v5.6) as provided by JGI and stored in Biostrings objects. The data in this package is public. See citation("BSgenome.Creinhardtii.JGI.v5.6") for how to cite in publications.

This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.

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.

bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods.

Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm2, 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 (taeGut1, Jul. 2008) and stored in Biostrings objects.

This package provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.

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 Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects.

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

This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading.

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

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects.