This package provides tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.

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 provides a test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

This package extracts tandem mass spectrometry (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. It also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.

This package provides a client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various administrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT (K-acetyl-transferases) family. Lysine acetylation is a well-studied posttranslational modification on kinds of proteins. About four thousand lysine acetylation sites and over 20 lysine KATs have been identified. However, which KAT is responsible for a given protein or lysine site acetylation is mostly unknown. In this package, we use a GSEA-like (Gene Set Enrichment Analysis) method to make predictions. GSEA method was developed and successfully used to detect coordinated expression changes and find the putative functions of the long non-coding RNAs.

This package adductomicsR processes data generated by the second stage of mass spectrometry (MS2) to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies level mass spectral peaks from first stage of mass spectrometry (MS1) data.

This package provides an array-like container for convenient access and manipulation of HDF5 datasets. It supports delayed operations and block processing.

This package provides a differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test, a Kruskal-Wallis test, a generalized linear model, or a correlation test. All tests report p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs.

This package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. It also contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data like gene expression/RNA sequencing/methylation/brain imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.

This is a package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

This package provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale function but avoids explicit realization of a dense matrix during block processing. This permits greater efficiency in common operations, most notably matrix multiplication.

The package xmapbridge can plot graphs in the X:Map genome browser. X:Map uses the Google Maps API to provide a scrollable view of the genome. It supports a number of species, and can be accessed at http://xmap.picr.man.ac.uk. This package exports plotting files in a suitable format. Graph plotting in R is done using calls to the functions xmap.plot and xmap.points, which have parameters that aim to be similar to those used by the standard plot methods in R. These result in data being written to a set of files (in a specific directory structure) that contain the data to be displayed, as well as some additional meta-data describing each of the graphs.

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 provides an expressionSet containing gene expression data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia.

This package provides S4 generic functions modeled after the matrixStats API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

This package implements methods to remove unwanted variation (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. birta (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of transcription factors and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.

This package provides functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests.

TreeSummarizedExperiment extends SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.

This package provides a suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means.