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 |