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

HarteminkLab/TOP documentation built on July 27, 2023, 6:14 p.m.