v0.2.7

• prepare_results.R for leafviz received a significant re-write including
  • Removed dependence on bedtools
  • Friendlier CLI arguments
  • New documentation on the doc website
• smart initialization got regularization (deals with co-linear covariates) and robustness to a rare divide-by-zero bug.

v0.2.6

• Changed PSI and deltaPSI calculations to better match empirical and be consistent across runs (issue #41)

v0.2.5

• Important bugfix for smart initialization when there are no technical/confounding covariates.

v0.2.4

• LeafViz PCA now made with ratios rather than counts
• prepare_results now accepts covariates in support file
• Added magrittr and stringr dependencies
• LeafViz now allows colour and shape of points in PCA to be set to group or covariate

v0.2.3

• Better control of Differential splicing initialization: the default "smart" initialization is now a one-shot method of moments estimator for the null model regression coefficients, but random initialization can be optionally specified, along with the seed (see --init and --seed options of leafcutter_ds.R) (issue #33)
• Dalila Pinto contributed a new script 'gtf2leafcutter.pl' for more robustly converting GTF files to the "annotation code" needed for leafviz. Thanks!

v0.2.2

• cluster_table now includes p.adjust column calculated using BH FDR control.
• Improved gene view in LeafViz
• check.names = F when reading counts files to avoid issues with sample file names getting changed by R
• Removed -w option from shebang in perl scripts since this was causing issues on Linux (fine on Mac)

v0.2

• Merged covariates branch, allow for controlling for confounders.
• Merged newstansyntax branch, reduces warnings from rstan.
• Added leafvis shiny app.