started modification of processing pipeline for new genome alignment
finished with raw_process.R function for new genome alignment
added new functionality - plot gene time courses normalized by gene length
edited and finished functionality - plot gene time courses normalized by gene length
edited diff-expr.R for new alignment; next step - to edit go.R for the same purpose - check all.genes.arg in go.R, I may need to use all 64000 genes instead of 32000 I am using at the moment
checked all.genes.arg in go.R, at first view there is no difference between using 64000 genes instead of 32000 I am using at the moment - need to check in Webgestalt again to be completely sure
finished with checking new alignment - will still keep fresh_alignment branch for a while. Finished with alt-splicing.R script - implemented it with parallelization
wrote plot_exons function in plot.R to visualize exon differential expression; did some processing of hg19 bam files for ismara
edited svd functions to get better figures for the paper; added svd analysis of egf genes to main.R function
added linc_rna function which filters out lincRNA genes from ki&pten genes and plot their time courses
edited some axis labels in svd.R functions - they were incorrect
edited some plot labels in main.R function for the manuscript
added new function to plot and export go term names ordered by their p-value
edited s_v_d_ismara function; wrote get_ismara_targets function; cleaned the files
worked on ismara activity profiles and  s_v_d_ismara function
added more analysis of ISMARA in main.R; added Kolmogorov-Smirnov and Wilcox tests for comparing motif-target scores distributions
finished with differential motif target activity
small update
small update