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.

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 genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects.

Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet.

Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects.

Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

R interface for importing and analyzing enzyme information from the BRENDA database.

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.

An small dataset that can be used to run examples from the beadarray vignette and examples.

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau4, 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 Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.

Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.

Full genome sequences for Gasterosteus aculeatus (Stickleback) as provided by UCSC (gasAcu1, Feb. 2006) and stored in Biostrings objects.

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro6, Jan. 2018) 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.

Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet.

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 Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects.

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.

Model-based analysis of single-cell methylation data.

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

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 Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects.

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.