d0d3b839e330ed6c8fb5935c157949c2 *DESCRIPTION
6a44c9109496f0830397a67c3e1abe1d *LICENSE
7aac0e2cbba18605815bb51e3f3bff5f *NAMESPACE
941225c3c4d5e5a5253d1959446cc8da *NEWS.md
a4c4c7474d71b8b0369c828ca0344377 *R/RcppExports.R
da7113070abffa1f5c451f092fdeeb24 *R/base-transcription-rates-class.R
d73ab95c774963232fe1e938200bc241 *R/experiment_transcription_rates-class.R
602f66e9cba4c8b2d42ec9e3874d7c41 *R/nascent_seq_preprocessing_helpers.R
26d7e9728ae5f4c83165c460b302924b *R/rate_estimation_helpers.R
cf5d3b6446af8d0a386afd5aa97f45ff *R/rate_estimation_two_conditions_helpers.R
5838d7099b80f262fbeb4e1f500c677f *R/rcpp_interface.R
7823fbe01d1cb632725ac6be98e4e445 *R/simulate_polymerase-class.R
32bbcb83d79fa13fdfea1a518b273b30 *R/simulation_transcription_rates-class.R
6780d316631eba1a63bf92e0995a54ab *R/transcription_rates_lrt-class.R
0cd95457b8441ad0dd907830348da175 *README.Rmd
e6e48728e53118d6f64717f7f8140127 *README.md
c48b86c9746231e155976c2d6377f0a7 *build/vignette.rds
2a41c393a50a801b56de2b0a8b2c86b2 *inst/CITATION
98c78b7604596bae5e646e0d0618bc88 *inst/doc/STADyUM_LRT_Tutorial.R
125af3c0d42eda0610772c4bc133e58e *inst/doc/STADyUM_LRT_Tutorial.Rmd
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dd3a128229eda79587792bbac511211b *inst/extdata/PROseq-DLD1-aoi-NELFC_Auxin-SE_minus_chr21_subset.bw
a69f9afacf3848a070f1f133d4fa8aff *inst/extdata/PROseq-DLD1-aoi-NELFC_Auxin-SE_plus_chr21_subset.bw
02215c629c9c1477ffe3a5b60017b6b2 *inst/extdata/PROseq-DLD1-aoi-NELFC_Auxin_Ctrl-SE_minus_chr21_subset.bw
1f01755242d2d807cb52c90b5ab55245 *inst/extdata/PROseq-DLD1-aoi-NELFC_Auxin_Ctrl-SE_plus_chr21_subset.bw
896967117db498b4e729d5c6d72139fc *inst/extdata/granges_for_read_counting_DLD1_chr21.RData
fc3e33ebbc8a955a9900fc73d251387f *inst/extdata/spikein_scaling_factor.csv
c1b485a55d0c387277753adde5294831 *inst/scripts/data_generation.txt
155e249788e65813850fcca44947ff66 *man/ExperimentTranscriptionRates-class.Rd
46654b152aa23e9ce9f46420742eb6fe *man/SimulatePolymerase-class.Rd
7cf32391c07c319b8d6430204d02a691 *man/SimulationTranscriptionRates-class.Rd
1e7b535ee01396fbb32afb441319ed0b *man/TranscriptionRates-class.Rd
ea399c815dbbcc68cc159c36eea541bd *man/TranscriptionRatesLRT-class.Rd
0820f0a8f3f2782a8e4ba526347b25de *man/estimateTranscriptionRates.Rd
ea71a99a56fbfe6ce213059088982b09 *man/getSdGroupCutoff.Rd
fd0970ac304aa876851b0e52909a2293 *man/rates.Rd
64cb35e1469f4320453f090e156f2069 *man/show-ExperimentTranscriptionRates-method.Rd
b8ce577b6f66221512f4ba4ac989d67e *man/stericHindrance.Rd
04d09a68a1fc08bc9efea8687ac579e2 *src/RcppExports.cpp
1a88926feea78a97c1c915dcac47a8fd *src/simPol.cpp
c39aa0047cf7d4be8a8ee280c3e30ea9 *src/simPol.h
22e0fe8090d44ec09ec6f1dea3acddf5 *tests/testthat.R
e909d77198ea4874377e8b29e0f6f962 *tests/testthat/test_exp_lrts.R
d3cab055b3991e87220e6abbb8488e57 *tests/testthat/test_sim_lrts.R
125af3c0d42eda0610772c4bc133e58e *vignettes/STADyUM_LRT_Tutorial.Rmd
c73b5e9a5dabec1d0e39c1e81fba4138 *vignettes/STADyUM_Rate_Estimation_Tutorial.Rmd
b7a13ee2b993023995cf3228162c9333 *vignettes/STADyUM_Simulator_Tutorial.Rmd
7c19d144710cc57c94ad3609aca174dd *vignettes/lrt_figures.png
d297c35c89357cf54b40f4510fafbe00 *vignettes/references.bib
2ad4e70ec4b110356f156604fa54a4b3 *vignettes/simpol_figures.png
