Files in andreaskapou/BPRMeth-devel
Model higher-order methylation profiles
.Rbuildignore
.gitignore
BPRMeth-devel.Rproj
DESCRIPTION
NAMESPACE
R/BPRMeth_package.R
R/RcppExports.R
R/basis_functions.R
R/betareg.R
R/betareg_cluster_wrap.R
R/betareg_optimize.R
R/blr.R
R/blr_cluster.R
R/bpr.R
R/bpr_bayes.R
R/bpr_bayes_predict_wrap.R
R/bpr_cluster_wrap.R
R/bpr_diff_classify_wrap.R
R/bpr_diff_eval_predict_wrap.R
R/bpr_diff_predict_wrap.R
R/bpr_diff_test_data_wrap.R
R/bpr_diff_test_wrap.R
R/bpr_optimize.R
R/bpr_predict_wrap.R
R/classification_model_diff_gex.R
R/create_methyl_region.R
R/create_prom_region.R
R/data.R
R/design_matrix.R
R/evaluate_functions.R
R/plotting_functions.R
R/pool_bs_seq_rep.R
R/preprocess_bs_seq.R
R/preprocess_final_HTS_data.R
R/process_bismark_beatson_wrap.R
R/process_haib_caltech_wrap.R
R/read_bs_bismark_cov.R
R/read_bs_encode_haib.R
R/read_bs_sc.R
R/read_chrom_size.R
R/read_encode_cgi.R
R/read_rna_beatson.R
R/read_rna_encode_caltech.R
R/regression_model_gex.R
R/sc_bayes_bpr_fdmm.R
R/sc_bayes_bpr_fdmm_old.R
R/sc_bpr_cluster_wrap.R
R/utils.R
README.md
data-raw/create_data.R
data/gex_data.rda
data/lm_data.rda
data/meth_data.rda
inst/NEWS.Rd
inst/doc/BPRMeth_vignette.R
inst/doc/BPRMeth_vignette.Rnw
inst/doc/BPRMeth_vignette.bib
inst/doc/BPRMeth_vignette.pdf
inst/doc/model-bpr.pdf
inst/extdata/hg19.chr.sizes
inst/extdata/rnaseq.bed
inst/extdata/rrbs.bed
man/BPRMeth.Rd
man/betareg_cluster_wrap.Rd
man/betareg_model.Rd
man/betareg_optimize.Rd
man/blr.Rd
man/blr_cluster.Rd
man/boxplot_cluster_gex.Rd
man/bpr_EM_fast.Rd
man/bpr_bayes.Rd
man/bpr_bayes_predict_wrap.Rd
man/bpr_cluster_wrap.Rd
man/bpr_diff_classify_wrap.Rd
man/bpr_diff_eval_predict_wrap.Rd
man/bpr_diff_predict_wrap.Rd
man/bpr_diff_test_data_wrap.Rd
man/bpr_diff_test_wrap.Rd
man/bpr_model.Rd
man/bpr_optimize.Rd
man/bpr_predict_wrap.Rd
man/create_basis.Rd
man/create_methyl_region.Rd
man/create_prom_region.Rd
man/design_matrix.Rd
man/eval_functions.Rd
man/gex_data.Rd
man/lm_data.Rd
man/meth_data.Rd
man/plot_cluster_prof.Rd
man/plot_fitted_profiles.Rd
man/plot_scatter_gex.Rd
man/pool_bs_seq_rep.Rd
man/predict.blr.Rd
man/predict_classification_model.Rd
man/predict_model_gex.Rd
man/preprocess_bs_seq.Rd
man/preprocess_final_HTS_data.Rd
man/print.blr.Rd
man/print.summary.blr.Rd
man/process_bismark_beatson_wrap.Rd
man/process_haib_caltech_wrap.Rd
man/read_bs_bismark_cov.Rd
man/read_bs_encode_haib.Rd
man/read_bs_sc.Rd
man/read_chrom_size.Rd
man/read_encode_cgi.Rd
man/read_rna_beatson.Rd
man/read_rna_encode_caltech.Rd
man/sc_bayes_bpr_fdmm.Rd
man/sc_bayes_bpr_fdmm_old.Rd
man/sc_bpr_cluster_wrap.Rd
man/summary.blr.Rd
man/train_classification_model.Rd
man/train_model_gex.Rd
src/.gitignore
src/RcppExports.cpp
src/bpr_func.cpp
tests/testthat.R
tests/testthat/test-basis.R
tests/testthat/test-bpr.R
tests/testthat/test-design_matrix.R
tests/testthat/test-eval_function.R
tests/testthat/test-utils.R
vignettes/BPRMeth_vignette-concordance.tex
vignettes/BPRMeth_vignette.R
vignettes/BPRMeth_vignette.Rnw
vignettes/BPRMeth_vignette.bib
vignettes/BPRMeth_vignette.pdf
vignettes/BPRMeth_vignette.tex
vignettes/model-bpr.pdf
