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

This package contains functions for exploratory oligonucleotide array analysis.

DEComplexDisease is designed to find the DEGs for complex disease, which is characterized by the heterogeneous genomic expression profiles. Different from the established DEG analysis tools, it does not assume the patients of complex diseases to share the common DEGs. By applying a bi-clustering algorithm, DEComplexDisease finds the DEGs shared by as many patients. Applying the DEComplexDisease analysis results, users are possible to find the patients affected by the same mechanism based on the shared signatures.

This package AMARETTO represents an algorithm that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. AMARETTO can be applied in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer pathways.

tRNAdbImport imports the entries of the tRNAdb and mtRNAdb as GRanges object.

This package provides raw beta values from 36 samples across 3 groups from Illumina 450k methylation arrays.

This package implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.

The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.

This package exposes an annotation database generated from Ensembl.

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

This package provides summarized MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects.

This R package is for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis, such as differential gene expression or transcript usage.

This is the classification package for the automated analysis of Affymetrix arrays.

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

This package offers simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. It works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs, etc). Requires DNA quantitation data or sequenced negative control samples.

The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

This package provides statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package. The three models admit blocking factors to control for nuisance variables. To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

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.

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.

This package provides full genome sequences for Homo sapiens from 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.

This package provides a package containing an environment representing the HG_U95Av2.CDF file.

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is a free cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

This package implements widgets to provide user interfaces.