This package provides a package containing an environment representing the Barley1.CDF file.

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

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

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).

Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.

Full genome sequences for Cryptococcus neoformans var. grubii KN99 (assembly ASM221672v1 assembly accession GCA_002216725.1).

This package provides a tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.

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.

Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr11, Feb. 2017) and stored in Biostrings objects.

Full genome sequences for Arabidopsis thaliana as provided by TAIR (snapshot from April 23, 2008) and stored in Biostrings objects.

Genetic algorithm are a class of optimization algorithms inspired by the process of natural selection and genetics. This package allows users to analyze and optimize high throughput genomic data using genetic algorithms. The functions provided are implemented in C++ for improved speed and efficiency, with an easy-to-use interface for use within R.

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

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) 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.

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.

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

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

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects.

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

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.

`BatchSVG` is a feature-based Quality Control (QC) to identify SVGs on spatial transcriptomics data with specific types of batch effect. Regarding to the spatial transcriptomics data experiments, the batch can be defined as "sample", "sex", and etc.The `BatchSVG` method is based on binomial deviance model (Townes et al, 2019) and applies cutoffs based on the number of standard deviation (nSD) of relative change in deviance and rank difference as the data-driven thresholding approach to detect the batch-biased outliers.

From the perspective of metabolites as the continuation of the central dogma of biology, metabolomics provides the closest link to many phenotypes of interest. This makes metabolomics research promising in teasing apart the complexities of living systems. However, due to experimental reasons, the data includes non-biological variation which limits quality and reproducibility, especially if the data is obtained from several batches. The batchCorr package reduces unwanted variation by way of between-batch alignment, within-batch drift correction and between-batch normalization using batch-specific quality control samples and long-term reference QC samples. Please see the associated article for more thorough descriptions of algorithms.

Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac2, 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. NOTE: In most assemblies available at UCSC, Tandem Repeats Finder repeats were filtered to retain only the repeats with period <= 12. However, the filtering was omitted for this assembly, so the TRF masks contain all Tandem Repeats Finder results.

Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object.