This is a literate presentation demonstrating the use of Emacs, R and Sweave to generate reports from bioinformatics data. The master file in all this is the .Rnw! To compile it to .tex simply issue the command R CMD Sweave emacs-envir.Rnw compile the .tex file to dvi or pdf using whatever command you prefere on the .tex file Dependencies: Bioperl R R ggplot R BioConductor Short read (see http://www.bioconductor.org/packages/bioc/html/ShortRead.html) blastall (see below) Dependencies not easyly resolvable: The local blast-databases. Therefore the actual blastsearches are commented out in the script pilot.pl and two files are supplied as surrogates. To be more precise these blastsearches are carried out by a script called cobl.pl. the use of this script is completly turned of at the moment. I will in future try to include the Databases, or to find something else to p rovide reproducibility to that level, like possible only on my machine at the moment. In the meantime you can get the Databases on request. (The raw data is needed for pilot.pl). My R sessionInfo > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ggplot2_0.8.3 reshape_0.8.3 plyr_0.1.9 proto_0.3-8 [5] ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.0 Biostrings_2.14.2 [9] IRanges_1.4.4 loaded via a namespace (and not attached): [1] Biobase_2.6.0 hwriter_1.1