This package implements a method to analyze single-cell RNA-seq data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display copy number variation. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.

Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.

This package provides a package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes. This is done by exploring expression intensity of genes across positions of a tumor genome in comparison to a set of reference "normal" cells. A heatmap is generated illustrating the relative expression intensities across each chromosome, and it often becomes readily apparent as to which regions of the tumor genome are over-abundant or less-abundant as compared to that of normal cells.

This package provides tools to detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

This package provides functions for plotting genomic data.

This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

This package provides R environments for the annotation of microarrays.

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

This package provides a collection of functions and classes which serve as the foundation for packages such as PharmacoGx and RadioGx. It was created to abstract shared functionality to increase ease of maintainability and reduce code repetition in current and future Gx suite programs. Major features include a CoreSet class, from which RadioSet and PharmacoSet are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating AUC or SF are included.

This package provides tools for the computationally efficient analysis of quantitative trait loci (QTL) data, including eQTL, mQTL, dsQTL, etc. The software in this package aims to support refinements and functional interpretation of members of a collection of association statistics on a family of feature/genome hypotheses.

This package provides lower-level functionality to interface with Google Cloud Platform tools. gcloud and gsutil are both supported. The functionality provided centers around utilities for the AnVIL platform.

This package provides utilities for Receiver Operating Characteristic (ROC) curves, with a focus on micro arrays.

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

This package provides functions to plot data associated with arbitrary genomic intervals along chromosomal ideogram.

This package implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. It includes a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.

This package provides Affymetrix HG-U133_Plus_2 array annotation data (chip hgu133plus2) assembled using data from public repositories.

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. The ggcyto wrapper and some custom layers also make it easy to add gates and population statistics to the plot.

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

This package provides a collection of functions for left-censored missing data imputation. Left-censoring is a special case of missing not at random (MNAR) mechanism that generates non-responses in proteomics experiments. The package also contains functions to artificially generate peptide/protein expression data (log-transformed) as random draws from a multivariate Gaussian distribution as well as a function to generate missing data (both randomly and non-randomly). For comparison reasons, the package also contains several wrapper functions for the imputation of non-responses that are missing at random.

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.