Saturday, October 20, 2012

Bioconductor - BiocGenerics + basic install for Bioconductor v11

A few useful commands to get your Bioconductor to level2:
Besides the nice upgrade command:


* biocLite("BiocUpgrade")

* biocLite("BiocGenerics") : basic functions needed by many packages.(manual can be obtained here)

ALSO of interest for NGS: Consider batch-installing a number of must-have:

* biocLite(c('affy' 'affyPLM' 'annmap' 'annotate' 'AnnotationDbi'
'AnnotationForge' 'beadarray' 'Biobase' 'biocGraph' 'Biostrings' 'biovizBase'
'Category' 'categoryCompare' 'cghMCR' 'ChIPpeakAnno' 'chipseq' 'ChromHeatMap'
'cn.mops' 'codelink' 'crlmm' 'cummeRbund' 'EDASeq' 'eisa' 'fastseg' 'ffpe'
'flowCore' 'flowFP' 'flowMerge' 'flowQ' 'flowStats' 'frma' 'GenomicFeatures'
'GenomicRanges' 'GGBase' 'ggbio' 'GGtools' 'graph' 'GSEABase' 'GSVA' 'Gviz'
'HTSeqGenie' 'IRanges' 'KEGGdzPathwaysGEO' 'LVSmiRNA' 'MEDIPS' 'methylumi'
'minfi' 'MinimumDistance' 'MiRaGE' 'MotifDb' 'MotIV' 'nucleR' 'oligo'
'oligoClasses' 'OrganismDbi' 'pcaMethods' 'PICS' 'PING' 'prada'
'R453Plus1Toolbox' 'RCytoscape' 'REDseq' 'Repitools' 'RGalaxy' 'Ringo' 'rMAT'
'Rsamtools' 'rsbml' 'rtracklayer' 'ShortRead' 'simpleaffy' 'SLGI' 'snpStats'
'Streamer' 'tigre' 'triform' 'TSSi' 'VariantAnnotation' 'VariantTools' 'XDE'))

Fwd: please follow footer link

* Finally, a nice tutorial from a recent Bioconductor CSC2012 training can be found with attached material (here);

Bioconductor - 2012: Next generation sequencing data analysis with R/Bioconductor

June, CSC IT Center For Science, Espoo, Finland
This course by Dr Martin Morgan covers R/Bioconductor functionality for several aspects of next generation sequencing data analysis, ranging from RNA-seq and ChIP-seq data analysis to variant annotation. The course consists of lectures and hands-on exercises, and it is targeted for people who already have experience with the R statistical programming language.

(Original Post: