f3e0c2165ee68f4796f22fb4cfe2522d *DESCRIPTION
6a44c9109496f0830397a67c3e1abe1d *LICENSE
b6394f736cadd63fb8774cf08896099d *NAMESPACE
941225c3c4d5e5a5253d1959446cc8da *NEWS.md
a4c4c7474d71b8b0369c828ca0344377 *R/RcppExports.R
2e38936cd0dc47b022e626918633e0de *R/base-transcription-rates-class.R
fd28a2749e8d0f71bb63fcf811072c6c *R/experiment_transcription_rates-class.R
f5575b6f03735bd89503090938e1f8bb *R/rate_estimation_helpers.R
efcf765dd5e1f90541890309882de88c *R/rate_estimation_two_conditions_helpers.R
5838d7099b80f262fbeb4e1f500c677f *R/rcpp_interface.R
7823fbe01d1cb632725ac6be98e4e445 *R/simulate_polymerase-class.R
df71e2540edff1cedf15189946318e37 *R/simulation_transcription_rates-class.R
3791bdb57b87eeb76a44cd9b33a60bb0 *R/transcription_rates_lrt-class.R
bb12faaf668dd64a4326da3d1c664a81 *README.Rmd
1bce6d811f104a302e29e6598c4afcd4 *README.md
5af3c2e2b48af2ee2c46b10ebcb4fb55 *build/vignette.rds
877428c97d8a394ee0beb17d3e8bc4a5 *inst/CITATION
d8af3af1fb0ec16f5a8326bf43fdad8b *inst/doc/STADyUM.R
453a6fbaf5ee4a1b72c2271acd145311 *inst/doc/STADyUM.Rmd
5109b0211b66cf350998320ddfd79c46 *inst/doc/STADyUM.html
de846d31f4aafc5c5a68c7b8b25d49d8 *inst/extdata/PROseq-DLD1-aoi-NELFC_Auxin-SE_minus_chr21.bw
d9464487d415d498906d68a2f6d6e758 *inst/extdata/PROseq-DLD1-aoi-NELFC_Auxin-SE_plus_chr21.bw
0d57354312edaf018c1c27c5ee760fa3 *inst/extdata/PROseq-DLD1-aoi-NELFC_Auxin_Ctrl-SE_minus_chr21.bw
0c7a96cc600ffc708ff2fb12f930072c *inst/extdata/PROseq-DLD1-aoi-NELFC_Auxin_Ctrl-SE_plus_chr21.bw
cf44ab2e3050c6d21b792cf507cb3f50 *inst/extdata/granges_for_read_counting_DLD1_chr21.RData
fc3e33ebbc8a955a9900fc73d251387f *inst/extdata/spikein_scaling_factor.csv
2780edfcf1e19f86ee956c2265062779 *inst/scripts/data_generation.txt
9e658090f16d4c336497c103135a5082 *man/ExperimentTranscriptionRates-class.Rd
46654b152aa23e9ce9f46420742eb6fe *man/SimulatePolymerase-class.Rd
7cf32391c07c319b8d6430204d02a691 *man/SimulationTranscriptionRates-class.Rd
a0568759fb038eb3c5df4a708cacf81c *man/TranscriptionRates-class.Rd
3c9c4d0ec73779000747267ce2f9044e *man/TranscriptionRatesLRT-class.Rd
4fb72ea4b4472dea19b2a7e04ce5f14c *man/estimateTranscriptionRates.Rd
47e6a4414a844428845b0871aae85e92 *man/rates.Rd
64cb35e1469f4320453f090e156f2069 *man/show-ExperimentTranscriptionRates-method.Rd
715082188913615ef56892ed04427703 *man/stericHindrance.Rd
04d09a68a1fc08bc9efea8687ac579e2 *src/RcppExports.cpp
1a88926feea78a97c1c915dcac47a8fd *src/simPol.cpp
c39aa0047cf7d4be8a8ee280c3e30ea9 *src/simPol.h
22e0fe8090d44ec09ec6f1dea3acddf5 *tests/testthat.R
a22791a34b4c39c3a5e652d392b3972d *tests/testthat/test_exp_lrts.R
c989541c9b0e3c2968cfb78070aa304c *tests/testthat/test_sim_lrts.R
453a6fbaf5ee4a1b72c2271acd145311 *vignettes/STADyUM.Rmd
067026769719b372b4d3131b210c6257 *vignettes/references.bib
b899ebf229379c645ef6be15db2c4e5c *vignettes/simBetaViolinPlot.png
afc381246f572e569232f428dfba7a38 *vignettes/simPauseSitesContourMap.png
2ad4e70ec4b110356f156604fa54a4b3 *vignettes/simpol_figures.png
