Files in andrewGhazi/malacoda
Bayesian Analysis of High-Throughput Genomic Assays
.Rbuildignore
.gitignore
.travis.yml
CRAN-RELEASE
DESCRIPTION
NAMESPACE
R/README.R
R/annotation_analysis.R
R/data.R
R/fitting_functions.R
R/importing_functions.R
R/malacoda-package.R
R/plotting_functions.R
R/prior_fitting.R
R/qc_functions.R
R/sampler_functions.R
R/stanmodels.R
R/traditional_analysis_functions.R
R/zzz.R
README.Rmd
README.md
Read-and-delete-me
cran-comments.md
data/activities_example.RData
data/barcode_by_id.RData
data/cond_prior_example.RData
data/dropout_example.RData
data/example_posterior.RData
data/example_result.RData
data/fastq_examples.RData
data/filtered_example_data.RData
data/marg_prior_example.RData
data/ratios_example.RData
data/u_deepsea.RData
data/umpra_example.RData
inst/include/meta_header.hpp
malacoda.Rproj
man/activities_example.Rd
man/barcode_by_id.Rd
man/compute_activities.Rd
man/compute_kl_est.Rd
man/cond_prior_example.Rd
man/count_barcodes.Rd
man/count_barcodes_in_fastq.Rd
man/cut_out_seqs.Rd
man/decode_errors.Rd
man/dropout_example.Rd
man/example_posterior.Rd
man/example_result.Rd
man/fastq_examples.Rd
man/figures/cond_hexs.png
man/figures/cond_prior_improvement.png
man/figures/interval_example.png
man/figures/kruschke_latex.png
man/figures/logo.png
man/figures/logo.svg
man/figures/malacoda_intervals.png
man/figures/mi_example.png
man/figures/mpra_corr.png
man/figures/noise_hexs.png
man/figures/posterior_beeswarm_example.png
man/figures/prior_types.png
man/figures/tile_example.png
man/find_prior_weights.Rd
man/fit_cond_prior.Rd
man/fit_dropout_model.Rd
man/fit_grouped_prior.Rd
man/fit_marg_prior.Rd
man/fit_mpra_model.Rd
man/fit_nb.Rd
man/generate_distance_matrix.Rd
man/get_kl_divergences.Rd
man/get_label_y.Rd
man/get_prior_ratios.Rd
man/get_sample_correlations.Rd
man/get_sample_depths.Rd
man/get_well_represented.Rd
man/increase_regularization.Rd
man/malacoda-package.Rd
man/malacoda_intervals.Rd
man/marg_prior_example.Rd
man/mpra_tile_plot.Rd
man/plot_dna_representation.Rd
man/plot_mpra_correlations.Rd
man/plot_prior_ratios.Rd
man/plot_prior_samples.Rd
man/plot_ratio_hexs.Rd
man/posterior_beeswarm.Rd
man/ratios_example.Rd
man/run_activity_tests.Rd
man/sample_from_prior.Rd
man/score_annotation.Rd
man/summarise_cond_prior.Rd
man/summarise_one_prior.Rd
man/summarise_prior_samples.Rd
man/supplements/S1_Appendix.html
man/supplements/S2_Appendix.html
man/supplements/S3_Appendix.html
man/supplements/readme_how_to_view.txt
man/trim_and_filter.Rd
man/u_deepsea.Rd
man/umpra_example.Rd
src/Makevars
src/Makevars.win
src/init.cpp
src/init.o
src/malacoda.so
src/stan_files/bc_mpra_fit_gamma.stan
src/stan_files/bc_mpra_model.hpp
src/stan_files/bc_mpra_model.o
src/stan_files/bc_mpra_model.stan
src/stan_files/bc_mpra_model_mle.stan
src/stan_files/chunks/license.stan
src/stan_files/dropout_model.hpp
src/stan_files/dropout_model.o
src/stan_files/dropout_model.stan
src/stan_files/monoallelic_model.stan
src/stan_files/tissue_model.stan
src/stan_files/weighted_gamma.stan
tools/make_cc.R
vignettes/mpra_vignette.Rmd
