This package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.

This package implements quantile smoothing. It contains a dataset used to produce human chromosomal ideograms for plotting purposes and a collection of arrays that contains data of chromosome 14 of 3 colorectal tumors. The package provides functions for painting chromosomal icons, chromosome or chromosomal idiogram and other types of plots. Quantsmooth offers options like converting chromosomal ids to their numeric form, retrieving the human chromosomal length from NCBI data, retrieving regions of interest in a vector of intensities using quantile smoothing, determining cytoband position based on the location of the probe, and other useful tools.

This package provides tools to identify cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.

This package implements a new RNA-Seq analysis method and integrates two modules: a basic model for pairwise comparison and a linear model for complex design. RNA-Seq quantifies gene expression with reads count, which usually consists of conditions (or treatments) and several replicates for each condition. This software infers differential expression directly by the counts difference between conditions. It assumes that the sum counts difference between conditions follow a negative binomial distribution. In addition, ABSSeq moderates the fold-changes by two steps: the expression level and gene-specific dispersion, that might facilitate the gene ranking by fold-change and visualization.

This package provides a set of annotation maps describing the entire Human Disease Ontology. The annotation data comes from https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology.

This package provides data from 6 samples across 2 groups from 450k methylation arrays.

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15.

Saves the delayed operations of a DelayedArray to a HDF5 file. This enables efficient recovery of the DelayedArray's contents in other languages and analysis frameworks.

This package provides a set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

This package provides a collection of software tools for calculating distance measures.

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, July 2007) and stored in Biostrings objects.

The package uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The package contains functions for combining the results of multiple runs of gene set analyses.

This package provides R functions for common pre-processing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.

This package implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.

This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data.

The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files.

This package performs multiple co-inertia analysis of omics datasets.

This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less pretty output than a vendor specific parser.

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data.

The purpose of this GO.db annotation package is to provide detailed information about the latest version of the Gene Ontologies.

This package identifies differential expression in high-throughput count data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.