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Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects.
Example whole genome bisulfite data for the bsseq package.
Full genome sequences for Glycine max as provided by NCBI (assembly Glycine_max_v4.0, assembly accession GCF_000004515.5) and stored in Biostrings objects.
derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549.
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.
Microarray analysis methods that use BufferedMatrix objects.
Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such as phosphoproteomics or transcriptomics, but it can be used for any data that can be represented by a 2D table, and has two sub populations within the table to compare.
Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) and stored in Biostrings objects.
It contains pre-compiled Gene Ontology gene sets for all organisms available on the Ensembl database. It also includes GO gene sets for organisms on Ensembl Plants, Ensembl Metazoa, Ensembl Fungi and Ensembl Protists. The data was collected with the biomaRt package.
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings objects.
This package provides a BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).
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 Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects.
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.
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.
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau6, 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.
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).
Full genome sequences for Mustela putorius furo (Ferret) as provided by UCSC (musFur1, Apr. 2011) and stored in Biostrings objects.
Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor.
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac8, Nov. 2015) and stored in Biostrings objects.
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects.
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 Mus musculus (Mouse) as provided by UCSC (genome mm39, based on assembly GRCm39) and stored in Biostrings objects.
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.