This package is an R implementation for fully unsupervised deconvolution of complex tissues. DebCAM provides basic functions to perform unsupervised deconvolution on mixture expression profiles by CAM and some auxiliary functions to help understand the subpopulation- specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.

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.

This package loads a TxDb object, which is an R interface to prefabricated databases contained in this package. This package provides the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) based on the knownGene track.

The polyester package simulates RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.

This package implements the gene expression anti-profiles method. Anti-profiles are a new approach for developing cancer genomic signatures that specifically take advantage of gene expression heterogeneity. They explicitly model increased gene expression variability in cancer to define robust and reproducible gene expression signatures capable of accurately distinguishing tumor samples from healthy controls.

This package provides functions for handling data from Bioconductor Affymetrix annotation data packages. It produces compact HTML and text reports including experimental data and URL links to many online databases. It allows searching of biological metadata using various criteria.

This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.

This package provides infrastructure shared by all Biostrings-based genome data packages and support for efficient SNP representation.

This package is designed to store minor allele frequency data. It retrieves this data from the Genome Aggregation Database (gnomAD version 3.1.2) for the human genome version GRCh38.

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

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

This package implements a method to rapidly assess cell type identity using both functional and random gene sets and it allows users to quantify cell type replicability across datasets using neighbor voting. MetaNeighbor works on the basis that cells of the same type should have more similar gene expression profiles than cells of different types.

This is a package for semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

This package provides a set of annotation maps describing the entire Disease Ontology.

This package provides a set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

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

Quickly find motif matches for many motifs and many sequences. This package wraps C++ code from the MOODS motif calling library.

This package provides Affymetrix Human Genome U95 Set annotation data (hgu95av2) assembled using data from public data repositories.

This is a package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

This package provides a collection of tools for performing category analysis.

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

This package provides infrastructure to store and access genome-wide position-specific scores within R and Bioconductor.

This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells. PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.

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.