- update README
- add Empirical studies section
- add pkgdown site
- fix factor level ordering for geneBodyCoverage plot
- save geneBodyCoverage as tsv
- adjust factor levels for number of inserts (#4)
- summarize number of inserts by transcript (#5)
- fix order of factors
- remove duplicate entries in psl input
- add plot of transcript length distributions conditioned on number of mapped contigs
- fix y axis for histogram plots
- increase point size of some plots
- summarizeGeneBodyCoverage and countSubjectsByCoverage now accept DataFrame inputs, obviating the need to rerun geneBodyCoverage multiple times in genecovr script
- Remove characters trailing first space in fasta headers
- Fix conversion of DNAStringSet to Seqinfo
- Make sure geneBodyCoverage table has nmax levels
- add depthOfCoverage function and analysis to vignette and script
- reduceHitCoverage is deprecated
- improve some docs
- add wrapper for saving plots
- add tests mainly for alignmentpairs and test setup