SigmaFC bug fix in depletion setting

Bugfix in gene depletion ranking using SigmaFC metric (removed obsolete damping function)

New gene ranking method

• added new gene ranking method (SigmaFC: sum of fold-changes)
• website allows upload of either sequencing data or count data
• supports svg output of all images produced (incl. scatterplots)
• added sgRNA density (contour) plots
• output folder structure re-organized
• autmatic highlighting of top10 genes in scatterplots
• fixed minor bugs with p-value computation
• Permutation number for STARS hard-set to 10 (to avoid long computation times)

Minor bug fixes

• Minor bug fix in custom library processing with numbers-only identifiers
• Minor bug fix in model selection with low control variance
• Minor bug fix in STARS output

Combination of replicates

• Combination of gene ranking p-values across replicates
• Averaging of sgRNA counts across replicates
• New gene ranking method based on average log fold-change
• Improved method for choosing between Poisson and neg. binomial model
• Automatic check for Python runtime errors in the log file
• Bug fix with sequence quality check of raw fastq files
• Table output format changed to .txt

Support for non-overdispersed data

• Algorithm will choose Poisson or neg. binomial model based on the amount of overdispersion in control counts
  *** All data in the manuscript based on this release! ***

flexible sgRNA sequence length

• sgRNA length can be defined by the user
• improved special character sanity check
• separate alphas for sgRNA and gene significance
• suppression of technical log output during index building
• added 'sidak' and 'bonferroni' options for multiple tests
• removed a bug in replicate plot when there are no non-targeting controls

Improved custom library support

added a library sanity check script to replace non-printable special characters in gene names

Status message upon completion

• added status message at end of completion (Results screen might take a minute to load)

Bugfix

• Bug fix in aRRA permutation test with small libraries

Bugfix

• changed the colors in axes3d (AlignReads) to RGB tupels (bug in matplotlib)