New and relevant packages
February 3, 2015
GenomicFiles() to coordinate on-disk files with
reduceBy*() to iterate over regions or files
reduceByYield() to iterate through files, e.g.,
seqlevels(), e.g., keep only standard chromsomes
keepStandardChromosomes()), place in standard order
sortSeqlevels()), rename (
- Standardize formatting
- HTML vignettes much more usable than PDF
findOverlaps(): significant performance improvements
- Quantitative variation in ChIP binding; differential binding between
treatment groups more relevant binding per se.
- See the Bioconductor
especially final question for statistical rationale and advanced
implementation (very interesting reading).
- SNVs from comparative shifts in non-consensus base call frequencies.
- Prediction, quantification and visualization of alternative
transcript events (rather than assessment of whole-transcript
- differential expression of assembled transcriptomes,
- base-level differential expression
- Impressive visualization of phylogenetic trees