Compensation description
Add link to DEPENDS file
Use FDR instead of Bonferroni for compensation p's
Merge branch 'readme' into develop
Replace hard-coded expression threshold
Reorder function definition to make it universal
Fix bug in `countsForConditions`, use norm. data
Test for enrichment of marks near expressed tRNAs

Use the Shen & al. data to test for the enrichment of certain enhancer
and other histone marks close to active tRNAs in embryo and adult liver.
Write p-value tables for Shen data
Add explanatory comment
Test for histone mark enrichment near DE tRNAs

Same as before, but for differentially expressed tRNAs rather than
upregulated tRNAs, again using the Shen & al. histone data.
Remove dead code
Fix error in Shen & al. analysis
Analyse codon/anticodon correlation with wobbling

First attempt at wobble pairing, which uses the data from the dos Reis
table. Since it turns out that this approach makes many assumptions
about the distribution of codon/anticodon pairing which are not
corroborated by data, we will subsequently attempt a different approach.

This is its own file rather than a separate branch since we want to make
both approaches available to reviewers in the main branch.
Move wobble analysis to subdirectory
Analyse codon/anticodon correlation with wobbling

Second attempt at analysis, using a more parsimonious scheme: assume
that all codons use their respective anticodon, unless that doesn’t
exist, in which case we use an alternative anticodon using wobble
pairing, and distribute that anticodon’s abundance on all its existing,
recognised codons based on their usage abundance.
Remove accidentally pasted code fragment
Refactor code by merging redundant functions

The three functions plotting the codon–anticodon correlation with
different methods (without wobbling, with wobbling in two variants)
perform almost exactly the same function and have been merged.
Comment was wrong, and let to an error in manuscript
Fix bug in `allDuplicated`

Make the function work even if there is not a single duplicate present.
Move to global definitions since it’s generally useful.