This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.

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 ofers functions for importation, normalization, visualization, and quality control to correct identified sources of variability in array of CGH experiments.

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

This is a package with metadata for fast genotyping Affymetrix GenomeWideSnp_6 arrays using the crlmm package.

This package provides R environments for the annotation of microarrays.

This package provides a framework for the quantification and analysis of short genomic reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.

The AffiXcan package imputes a genetically regulated expression (GReX) for a set of genes in a sample of individuals, using a method based on the total binding affinity (TBA). Statistical models to impute GReX can be trained with a training dataset where the real total expression values are known.

This package provides data needed to use the ITALICS package.

This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.

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

This is a package for creating na HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

This is a package for the assessment and comparison of the performance of risk prediction (survival) models.

This is a package that can be used for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

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.

MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.

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

This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.

This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.

This package provides a client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various administrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

This package provides gene-level read counts from RNA-Seq for gallein-treated and control zebrafish.

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 a database of PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137.

This package provides methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.