Files in andreaskapou/Melissa

Bayesian clustering and imputationa of single cell methylomes

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/Melissa_package.R R/melissa_gibbs.R R/melissa_vb.R R/process_data.R R/utils.R R/utils_plot.R README.md

data/melissa_encode_dt.rda

data/melissa_synth_dt.rda

inst/CITATION

inst/NEWS.Rd

inst/data-raw/create_synth_data.R inst/examples/analysis/experiment_design.rmd

inst/examples/analysis/model/figures/bayes-augment-probit-model.png

inst/examples/analysis/model/figures/melissa-model-small.png

inst/examples/analysis/model/figures/melissa-model.png

inst/examples/analysis/model/figures/melissa.png

inst/examples/analysis/model/figures/probit-mixture-model.png

inst/examples/analysis/model/figures/probit-model.png

inst/examples/analysis/model/melissa_model.Rmd inst/examples/analysis/mt_seq.Rmd inst/examples/analysis/smallwood_2014.Rmd inst/examples/analysis/synthetic.Rmd inst/examples/analysis/synthetic_encode_scRRBS.Rmd inst/examples/analysis/synthetic_encode_scWGBS.Rmd inst/examples/analysis/synthetic_pca_gmm_reviewer.Rmd

inst/examples/annotations/Nanog.bed

inst/examples/annotations/active_enhancers.bed

inst/examples/annotations/promoter.bed

inst/examples/annotations/super_enhancers.bed

inst/examples/clustering-imputation/mt-seq/deepcpg_impute_rep.R inst/examples/clustering-imputation/mt-seq/indep_impute_rep.R inst/examples/clustering-imputation/mt-seq/melissa_impute_rep.R inst/examples/clustering-imputation/mt-seq/rf_indep_impute_rep.R inst/examples/clustering-imputation/smallwood-2014/deepcpg_impute_rep.R inst/examples/clustering-imputation/smallwood-2014/indep_impute_rep.R inst/examples/clustering-imputation/smallwood-2014/melissa_impute_rep.R inst/examples/clustering-imputation/smallwood-2014/rf_indep_impute_rep.R inst/examples/clustering-imputation/synthetic/gmm_cell_eval_rep.R inst/examples/clustering-imputation/synthetic/gmm_cpg_eval_rep.R inst/examples/clustering-imputation/synthetic/gmm_var_eval_rep.R inst/examples/clustering-imputation/synthetic/indep_cell_eval_rep.R inst/examples/clustering-imputation/synthetic/indep_cpg_eval_rep.R inst/examples/clustering-imputation/synthetic/indep_var_eval_rep.R inst/examples/clustering-imputation/synthetic/melissa_cell_eval_rep.R inst/examples/clustering-imputation/synthetic/melissa_cpg_eval_rep.R inst/examples/clustering-imputation/synthetic/melissa_var_eval_rep.R inst/examples/clustering-imputation/synthetic/pca_gmm_cpg_eval_rep.R inst/examples/clustering-imputation/synthetic/rf_indep_cell_eval_rep.R inst/examples/clustering-imputation/synthetic/rf_indep_cpg_eval_rep.R inst/examples/clustering-imputation/synthetic/rf_indep_var_eval_rep.R inst/examples/clustering-imputation/synthetic/scRRBS/deepcpg_impute_rep.R inst/examples/clustering-imputation/synthetic/scRRBS/indep_impute_rep.R inst/examples/clustering-imputation/synthetic/scRRBS/melissa_impute_rep.R inst/examples/clustering-imputation/synthetic/scRRBS/rf_indep_impute_rep.R inst/examples/clustering-imputation/synthetic/scWGBS/deepcpg_impute_rep.R inst/examples/clustering-imputation/synthetic/scWGBS/indep_impute_rep.R inst/examples/clustering-imputation/synthetic/scWGBS/melissa_impute_rep.R inst/examples/clustering-imputation/synthetic/scWGBS/rf_indep_impute_rep.R inst/examples/clustering-imputation/synthetic/subsampled/deepcpg_impute_rep.R inst/examples/clustering-imputation/synthetic/subsampled/indep_impute_rep.R inst/examples/clustering-imputation/synthetic/subsampled/melissa_impute_rep.R inst/examples/clustering-imputation/synthetic/subsampled/rf_indep_impute_rep.R inst/examples/lib/melissa_gibbs.R inst/examples/lib/melissa_vb.R inst/examples/lib/utils.R inst/examples/lib/utils_plot.R inst/examples/model-efficiency/mt-seq/melissa_timing.R inst/examples/model-efficiency/smallwood-2014/melissa_timing.R inst/examples/model-efficiency/synthetic/model-efficiency.R inst/examples/model-selection/synthetic/model-selection.R inst/examples/preprocessing/README.Rmd inst/examples/preprocessing/mt-seq/compute_coverage.R inst/examples/preprocessing/mt-seq/create_promoter.R inst/examples/preprocessing/mt-seq/create_promoter_deepcpg.R inst/examples/preprocessing/mt-seq/create_region.R inst/examples/preprocessing/mt-seq/create_region_deepcpg.R inst/examples/preprocessing/mt-seq/filter_met.R inst/examples/preprocessing/mt-seq/filter_met_deepcpg.R inst/examples/preprocessing/mt-seq/met-state-distribution.R inst/examples/preprocessing/smallwood-2014/compute_coverage.R inst/examples/preprocessing/smallwood-2014/create_region.R inst/examples/preprocessing/smallwood-2014/create_region_deepcpg.R inst/examples/preprocessing/smallwood-2014/filter_met.R inst/examples/preprocessing/smallwood-2014/filter_met_deepcpg.R inst/examples/preprocessing/synthetic/download_hg38_gene_model.R inst/examples/preprocessing/synthetic/encode_cells.R inst/examples/preprocessing/synthetic/encode_coverage.R inst/examples/preprocessing/synthetic/encode_dissimilarity.R inst/examples/preprocessing/synthetic/encode_scWGBS_create_region.R inst/examples/preprocessing/synthetic/encode_scWGBS_create_region_deepcpg.R inst/examples/preprocessing/synthetic/encode_scWGBS_filter_met.R inst/examples/preprocessing/synthetic/encode_scWGBS_filter_met_deepcpg.R inst/examples/preprocessing/synthetic/encode_sc_create_region.R inst/examples/preprocessing/synthetic/encode_sc_create_region_deepcpg.R inst/examples/preprocessing/synthetic/encode_sc_deepcpg_filter_chr.R inst/examples/preprocessing/synthetic/encode_sc_filter_met.R inst/examples/preprocessing/synthetic/encode_sc_filter_met_deepcpg.R inst/examples/test/synth_impute_vb.R inst/examples/test/synth_infer_gibbs.R inst/examples/test/synth_infer_vb.R inst/examples/test/test_melissa_encode.R inst/examples/test/test_melissa_smallwood.R

inst/extdata/encode-coef.rds

inst/figures/melissa-model-small.png

inst/figures/melissa.png

man/Melissa.Rd man/binarise_files.Rd man/cluster_ari.Rd man/cluster_error.Rd man/create_melissa_data_obj.Rd man/eval_cluster_performance.Rd man/eval_imputation_performance.Rd man/extract_y.Rd man/filter_regions.Rd man/impute_met_files.Rd man/impute_test_met.Rd man/init_design_matrix.Rd man/log_sum_exp.Rd man/melissa_encode_dt.Rd man/melissa_gibbs.Rd man/melissa_synth_dt.Rd man/melissa_vb.Rd man/partition_dataset.Rd man/plot_melissa_profiles.Rd tests/testthat.R tests/testthat/test-filtering.R tests/testthat/test-running_melissa.R vignettes/process_files.Rmd vignettes/run_melissa.Rmd

andreaskapou/Melissa documentation built on June 12, 2020, 5:54 p.m.