This package contains functions and classes that are needed by arrayCGH packages.

This package provides robust model-based clustering using a t-mixture model with Box-Cox transformation.

This package provides full masked genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, 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.

This package provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA expression data sets.

This package provides a toolset for deciphering and managing biological sequences.

This package aims to provide a pipeline for the low-level analysis of gene expression microarray data, primarily focused on the Agilent platform, but which also provides utilities which may be useful for other platforms.

AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. AbseqR empowers the users of abseqPy with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.

Read bigWig and bigBed files using libBigWig. This package provides lightweight access to the binary bigWig and bigBed formats developed by the UCSC Genome Browser group.

The MBECS provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matrix (PFM), Position Weight Matrix (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

The SparseArray package is an infrastructure package that provides an array-like container for efficient in-memory representation of multidimensional sparse data in R. The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data, the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they support most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.

This package provides genome wide annotations for Zebrafish, primarily based on mapping using Entrez Gene identifiers.

This R package can annotate variants, compute amino acid coding changes and predict coding outcomes.

This package provides classes and statistical methods for large single-nucleotide polymorphism (SNP) association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies.

This package provides functions to compare two or more survival curves with:

• The Fleming-Harrington test for right-censored data based on permutations and on counting processes.

• An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.

This package provides functions to estimate a bipartite graph of protein complex membership using AP-MS data.

This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

This package provides a set of functions to create and interact with dynamic documents and vignettes.

This package provides a database of SIFT predictions for Homo sapiens dbSNP build 132.

This package provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.