Man pages for bartongroup/RATS
Relative Abundance of Transcripts

alloc_outCreate output structure.
annot2idsExtract matching transcript and gene IDs from a GTF file.
calculate_DTUSet up and execute the tests.
call_DTUCalculate differential transcript usage.
denest_sleuth_bootsExtract bootstrap counts into a less nested structure.
dtu_plurality_summarySummary of DTU plurality.
dtu_summarySummary of DTU calling.
dtu_switch_summarySummary of isoform switching events.
fish4rodentsImport abundances directly from salmon and kallisto output.
get_dtu_idsList of DTU ids.
get_plurality_idsList the gene IDs by number of isoforms showing significant...
get_switch_idsList of genes that switch isoform ranks.
group_samplesGroup samples by covariate value.
g.test.1Log-likelihood test of goodness of fit.
g.test.2Log-likelihood test of independence.
infer_bootnumRule-of-thumb number of iterations.
maxabsGet largest value by absolute comparison.
parameters_are_goodCheck input parameters.
plot_diagnosticsPlot diagnostics.
plot_genePlot abundances for all isoforms of a specified gene.
plot_overviewPlot DTU results overview.
plot_shiny_volcanoInteractive volcano plot, using shiny.
sim_boot_dataGenerate an artificial dataset of bootstrapped abundance...
sim_count_dataGenerate an artificial dataset of abundance estimates, for...
tidy_annotTidy up annotation.
bartongroup/RATS documentation built on May 21, 2018, 4:42 a.m.