New and relevant packages

Martin Morgan
February 3, 2015

Bioconductor packages

GenomicFiles

• GenomicFiles() to coordinate on-disk files with regions-of-intereset
• reduceBy*() to iterate over regions or files
• reduceByYield() to iterate through files, e.g., BamFile(..., yieldSize=1000000)

GenomeInfoDb

• Manipulate seqlevels(), e.g., keep only standard chromsomes (keepStandardChromosomes()), place in standard order (sortSeqlevels()), rename (renameSeqlevels())

BiocStyle

• Standardize formatting
• HTML vignettes much more usable than PDF
• Supports rmarkdown

(Rhtslib)

Bioconductor functionality

GenomicAlignments::readGAlignmentPairs() / readGAlignmentsList()

Rsamtools::pileup()

VariantAnnotation::VRanges()

findOverlaps(): significant performance improvements

AnnotationDbi::mapIds()

Contributed packages

csaw

• Quantitative variation in ChIP binding; differential binding between treatment groups more relevant binding per se.
• See the Bioconductor newsletter, especially final question for statistical rationale and advanced implementation (very interesting reading).

Rariants

• SNVs from comparative shifts in non-consensus base call frequencies.

SGSeq

• Prediction, quantification and visualization of alternative transcript events (rather than assessment of whole-transcript abundance).

ballgown

• differential expression of assembled transcriptomes,

derfinder

• base-level differential expression

AnalysisPageServer

• interactive reports(!)

ggtree

• Impressive visualization of phylogenetic trees

Etc.

• New packages summary (also posted to twitter)