Bioc ExperimentalDataNews

Overview

The ExperimentalDataNews blog brings out the huge value of ExperimentData packages in the Bioconductor ecosystem. These packages illustrate effectiveness of Bioc data structures in making outputs of influential experiments readily available for reanalysis or extended analysis, and for integration with other experiments. This page will give a table of contents, annotated with brief commentary on data structure strategies employed in key contributions.

Genetic regulation of genomic variation

1. dsQTL -- illustrates use of RangedSummarizedExperiment for DnaseI hypersensitivity (DHS) scoring on 1.4 million 100bp tiles, and describes how to use 1000 genomes genotypes to identify genetic loci associated with DHS.

2. geuvPack -- a RangedSummarizedExperiment for the FPKM of the first eQTL analysis of the GEUVADIS data (transcriptomics of Coriell cells from various HapMap populations).

3. yriMulti -- includes 450k methylation assays for YRI cohort members, and code for combining RNA-seq, 450k, and SNP genotyping data on this cohort into a MultiAssayExperiment instance.

Integrative genomics of human cancer

1. curatedTCGAData -- includes ~300 datasets, 11k patients, 33 cancers. Provides an easy-to-use interface function curatedTCGAData for creating MultiAssayExperiment objects from data types such as RNA-seq, mutation, copy number, methylation, GISTIC2, etc.