This package provides a database of PolyPhen predictions for Homo sapiens dbSNP build 131.

This package defines a BigMatrix ReferenceClass which adds safety and convenience features to the filebacked.big.matrix class from the bigmemory package. BigMatrix protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also protects against accidental data modification with a file-system-based permissions system. Utilities are provided for using BigMatrix-derived classes as assayData matrices within the Biobase package's eSet family of classes. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a BigMatrixFactor class, a file-backed matrix with factor properties.

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool.

This is a package for multivariate data analysis and graphical display of microarray data. Functions are included for supervised dimension reduction (between group analysis) and joint dimension reduction of two datasets (coinertia analysis).

This package extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

Microarray quality assessment is a major concern of microarray analysts. This package provides some simple approaches to in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics.

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.

The AffyRNADegradation package helps with the assessment and correction of RNA degradation effects in Affymetrix 3 expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

This package supports the computation of an F-test for the association between expression values and clinical entities. In many cases a two way layout with gene and a dichotomous group as factors will be considered. However, adjustment for other covariates and the analysis of arbitrary clinical variables, interactions, gene co-expression, time series data and so on is also possible. The test is carried out by comparison of corresponding linear models via the extra sum of squares principle.

This package provides methods for visualizing large multivariate datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. It includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.

This package segments single- and multi-track copy number data by a penalized least squares regression method.

This package provides examples and code that make use of the different graph related packages produced by Bioconductor.

This package provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.

This package implements functions for copy number variant calling, plotting, export and analysis from whole-genome single cell sequencing data.

This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.

This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.

The package r-alevinqc generates quality control reports summarizing the output from an alevin run. The reports can be generated as HTML or PDF files, or as Shiny applications.

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

This package provides SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be injected in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.

The goal of sansSouci is to perform post hoc inference: in a multiple testing context, sansSouci provides statistical guarantees on possibly user-defined and/or data-driven sets of hypotheses.

The package contains functions to infer and visualize cell cycle process using Single-cell RNA-Seq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. The tricycle provides a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, it also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.

This package performs multiple co-inertia analysis of omics datasets.

This package provides infrastructure for parallel computations distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation.