Tidied up. Removed unused functions.
wrote hd.R scripts for analyzing 8mer count data
further optimization of hd script
added parallel randomForest implementation
updated to match current workflow
updated bowtie2 and tophat2 for new naming conventions
update of strand project
major update
python bidirectional promoter finder, continued R rmd for science paper
before major edit
Added strand option to group.py/BAM
Updated group.py and BAMtoWIG.py with norm_by_mean option, which normalizes values by mean coverage across chromosome.