Files in HarteminkLab/TOP
Predict transcription factor occupancy using DNase- or ATAC-seq data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/assemble_training_data.R
R/backups.R
R/fit_models.R
R/plots.R
R/postfit_coef_samples.R
R/predict_occupancy.R
R/process_chip_data.R
R/process_dnase_atac_data.R
R/process_motif_sites.R
R/process_reads.R
README.Rmd
README.md
TOP.Rproj
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/data_preparation.html
docs/articles/index.html
docs/articles/predict_TF_occupancy_with_trained_model.html
docs/articles/predict_TF_occupancy_with_trained_model_files/figure-html/plot-predicted-measured-1.png
docs/articles/predict_TF_occupancy_with_trained_model_files/figure-html/plot-predicted-measured-middle-1.png
docs/articles/train_TOP_logistic_model.html
docs/articles/train_TOP_model.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/add_chip_peak_labels_to_sites.html
docs/reference/add_chip_signals_to_sites.html
docs/reference/assemble_training_data.html
docs/reference/bin_transform_counts.html
docs/reference/combine_TOP_samples.html
docs/reference/count_genome_cuts.html
docs/reference/count_normalize_chip.html
docs/reference/extract_TOP_coef_samples.html
docs/reference/extract_TOP_mean_coef.html
docs/reference/extract_tf_cell_combos.html
docs/reference/figures/schematic.png
docs/reference/fimo_motif_matches.html
docs/reference/fit_TOP_M5_model.html
docs/reference/get_sites_counts.html
docs/reference/get_total_reads.html
docs/reference/index.html
docs/reference/index_fa.html
docs/reference/merge_normalize_bin_transform_counts.html
docs/reference/merge_normalize_counts.html
docs/reference/millipede_binning.html
docs/reference/normalize_bin_transform_counts.html
docs/reference/normalize_chip.html
docs/reference/normalize_counts.html
docs/reference/plot_profile.html
docs/reference/plot_profile_strands.html
docs/reference/predict_TOP.html
docs/reference/process_candidate_sites.html
docs/reference/scatterplot_predictions.html
docs/reference/sort_index_idxstats_bam.html
docs/sitemap.xml
inst/extdata/example_data/CTCF.K562.ATAC.chip.example.data.rds
inst/extdata/model/TOP_M5_logistic_model.jags
inst/extdata/model/TOP_M5_model.jags
inst/extdata/trained_model_coef/ATAC/TOP_M5_posterior_mean_coef.rds
inst/extdata/trained_model_coef/ATAC/TOP_logistic_M5_posterior_mean_coef.rds
inst/extdata/trained_model_coef/DukeDnase/TOP_M5_posterior_mean_coef.rds
inst/extdata/trained_model_coef/DukeDnase/TOP_logistic_M5_posterior_mean_coef.rds
inst/extdata/trained_model_coef/UwDnase/TOP_M5_posterior_mean_coef.rds
inst/extdata/trained_model_coef/UwDnase/TOP_logistic_M5_posterior_mean_coef.rds
man/add_chip_peak_labels_to_sites.Rd
man/add_chip_signals_to_sites.Rd
man/assemble_training_data.Rd
man/bin_transform_counts.Rd
man/combine_TOP_samples.Rd
man/count_genome_cuts.Rd
man/count_normalize_chip.Rd
man/extract_TOP_coef_samples.Rd
man/extract_TOP_mean_coef.Rd
man/extract_tf_cell_combos.Rd
man/figures/schematic.png
man/fimo_motif_matches.Rd
man/fit_TOP_M5_model.Rd
man/get_sites_counts.Rd
man/get_total_reads.Rd
man/index_fa.Rd
man/merge_normalize_bin_transform_counts.Rd
man/merge_normalize_counts.Rd
man/millipede_binning.Rd
man/normalize_bin_transform_counts.Rd
man/normalize_chip.Rd
man/normalize_counts.Rd
man/plot_profile.Rd
man/plot_profile_strands.Rd
man/predict_TOP.Rd
man/process_candidate_sites.Rd
man/scatterplot_predictions.Rd
man/sort_index_idxstats_bam.Rd
vignettes/.gitignore
vignettes/data_preparation.Rmd
vignettes/predict_TF_occupancy_with_trained_model.Rmd
vignettes/train_TOP_logistic_model.Rmd
vignettes/train_TOP_model.Rmd
