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 Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal4, 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.

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

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.

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).

The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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 Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings objects.

This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome.

Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac3, Mar. 2009) and stored in Biostrings objects.

Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Sscrofa.UCSC.susScr3, 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 Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects.

Arabidopsis lyrata 8x Release [project ID 4002920] as provided by JGI ( snapshot from March 24, 2011) and stored in Biostrings objects.

The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.1101/525709v2 and https://pubmed.ncbi.nlm.nih.gov/33624743/, the results of module repertoire analyses can be represented in a fingerprint format, where red and blue spots indicate increases or decreases in module activity. These spots are subsequently represented either on a grid, with each position being assigned to a given module, or in a heatmap where the samples are arranged in columns and the modules in rows.

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.

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.

Example whole genome bisulfite data for the bsseq package.

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.

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.

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.

This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects.

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 12Xv2) and available at the URGI (INRA).