This is an R package to make it easier to import and store phylogenetic trees with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic trees with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

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

This package aggregateBioVar contains tools to summarize single cell gene expression profiles at the level of subject for single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates). A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools.

This package helps with the analysis of array CGH data by detecting of the breakpoints in the genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

This is a package to support identification of markers of rare cell types by looking at genes whose expression is confined in small regions of the expression space.

This package provides a GUI for analysis of Affymetrix microarray gene expression data using the affy and limma packages.

This package is a computational tool box for radio-genomic analysis which integrates radio-response data, radio-biological modelling and comprehensive cell line annotations for hundreds of cancer cell lines. The RadioSet class enables creation and manipulation of standardized datasets including information about cancer cells lines, radio-response assays and dose-response indicators. Included methods allow fitting and plotting dose-response data using established radio-biological models along with quality control to validate results. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating AUC or SF are included.

This package provides high performance functions for row and column operations on sparse matrices. Currently, the optimizations are limited to data in the column sparse format.

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 implements a method that aims to identify enhancers on large scale. The STARR-seq data consists of two sequencing datasets of the same targets in a specific genome. The input sequences show which regions where tested for enhancers. Significant enriched peaks i.e. a lot more sequences in one region than in the input where enhancers in the genomic DNA are, can be identified. So the approach pursued is to call peak every region in which there is a lot more (significant in a binomial model) STARR-seq signal than input signal and propose an enhancer at that very same position. Enhancers then are called weak or strong dependent of there degree of enrichment in comparison to input.

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.

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the "query space" or "reference space", and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.

This is a package for the automated analysis of Affymetrix arrays. It is used for preprocessing the arrays.

This package is used for the identification and validation of sequence motifs. It makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.

This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

The MassSpecWavelet package aims to process Mass Spectrometry (MS) data mainly through the use of wavelet transforms. It supports peak detection based on Continuous Wavelet Transform (CWT).

BiocSet displays different biological sets in a triple tibble format. These three tibbles are element, set, and elementset. The user has the ability to activate one of these three tibbles to perform common functions from the dplyr package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.

This package implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.

This package wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, 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.

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

This package implements some simple capabilities for representing and manipulating hypergraphs.