Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects.

Borealis is an R library performing outlier analysis for count-based bisulfite sequencing data. It detectes outlier methylated CpG sites from bisulfite sequencing (BS-seq). The core of Borealis is modeling Beta-Binomial distributions. This can be useful for rare disease diagnoses.

Full genome sequences for Monodelphis domestica (Opossum) as provided by UCSC (monDom5, Oct. 2006) and stored in Biostrings objects.

iFull genome sequences for Apis mellifera (Honey Bee) as provided by BeeBase (assembly4, Feb. 2008) 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).

This package provides a novel approach utilizing a homogeneous hidden Markov model. And effectively model untransformed beta values. To identify DMCs while considering the spatial. Correlation of the adjacent CpG sites.

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 8X) and available at the URGI (INRA). More details in Jaillon et al (Nature, 2007).

Full genome sequences for Asparagus officinalis (Garden asparagus) as provided by NCBI (Aspof.V1, Feb. 2017) 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 Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Tguttata.UCSC.taeGut1, 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). Both masks are "active" by default.

Full genome sequences for Drosophila virilis (assembly dvir_caf1, GenBank assembly accession GCA_000005245.1) as provided by Ensembl and stored in Biostrings objects.

Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau9, Apr. 2018) and stored in Biostrings objects.

Gene expression data from a breast cancer study published by Sotiriou 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.

Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer7, 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.

Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima.

Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor.

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

Full genome sequences for Cicer arietinum (Chickpea) as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects.

BreastSubtypeR provides an assumption-aware, multi-method framework for intrinsic molecular subtyping of breast cancer. The package harmonizes several published nearest-centroid (NC) and single-sample predictor (SSP) classifiers, supplies method-specific preprocessing and robust probe-to-gene mapping, and implements a cohort-aware AUTO mode that selectively enables classifiers compatible with the cohort composition. A local Shiny app (iBreastSubtypeR) is included for interactive analyses and to support users without programming experience.

This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).

Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan1, May 2012) and stored in Biostrings objects.

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.