The parody package provides routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

This package provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.

This package provides the data for the gene expression enrichment analysis conducted in the package ABAEnrichment. The package includes three datasets which are derived from the Allen Brain Atlas:

1. Gene expression data from Human Brain (adults) averaged across donors,

2. Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors, and

3. a developmental effect score based on the Developing Human Brain expression data.

All datasets are restricted to protein coding genes.

This package ADAMgui is a graphical user interface (GUI) for the ADAM package. The ADAMgui package provides two shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It's possible, for example, to choose a specific group of functionally associated genes (GFAG) and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and fold change can be easily seen with aid of the plots made with the GFAGpathUi function.

This package provides an R interface to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects.

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames.

The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

This package models a RESTful service as if it were a nested R list.

Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.

DSS is an R library performing differential analysis for count-based sequencing data. It detects differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

This package implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.

Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. This type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondence between different data sources.

iClusterPlus is developed for integrative clustering analysis of multi-type genomic data and is an enhanced version of iCluster proposed and developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise from the experiments where biological samples (e.g. tumor samples) are analyzed by multiple techniques, for instance, array comparative genomic hybridization (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so on. In the iClusterPlus model, binary observations such as somatic mutation are modeled as Binomial processes; categorical observations such as copy number states are realizations of Multinomial random variables; counts are modeled as Poisson random processes; and continuous measures are modeled by Gaussian distributions.

The anota2seq package provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources, translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source. Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels.

This package provides tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

The affyILM package is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behal of the Langmuir model.

This package provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.

This package provides tools to visualize oligonucleotide patterns and sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

The PSMatch package helps proteomics practitioners to load, handle and manage peptide spectrum matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE.

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.