Software

R/Bioconductor packages

BiocStyle Standard styles for vignettes and other Bioconductor documents
cellHTS2 Analysis of cell-based high-throughput screens
DEFormats Differential gene expression data formats converter
DESeq2 Differential gene expression analysis based on the negative binomial distribution
DEXSeq Inference of differential exon usage in RNA-Seq
EBImage Image processing and analysis toolkit for R
h5vc Managing alignment tallies using a hdf5 backend (by Paul Theodor Pyl, now at University of Copenhagen)
HilbertVis Visualize long vectors of data by means of Hilbert curves
imageHTS Analysis of high-throughput microscopy-based screens
rhdf5 HDF5 interface to R (by Bernd Fischer, now at DKFZ)
Rariant Identification and assessment of single nucleotide variants through shifts in non-consensus base call frequencies
RBioFormats R interface to the Bio-Formats library
shinyURL Save and restore the state of Shiny apps
SomaticSignatures Identification of mutational signatures of single nucleotide variants (SNVs)
tilingArray Transcript mapping with high-density oligonucleotide tiling arrays
vsn Normalization and variance stabilizing transformation of microarray data.

High-throughput sequencing

HTSeq A Python package for processing and analysing data from high-throughput sequencing assays

Visualization

HilbertVis Visualization of genomic data with the Hilbert curve

Data Packages

COSMIC.67 COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24)
Hiiragi2013 Experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oleś, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37.
doi: 10.1038/ncb2881
HD2013SGI Experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31.
doi: 10.1038/nmeth.2436
SomaticCancerAlterations Collection of somatic cancer alteration datasets