Files in CshlSiepelLab/DENR

Deconvolution of Expression for Nascent RNA Sequencing Data

LICENSE.md R/abundance_tables.R R/data_handling.R R/model_fit_statistics.R R/model_fitting.R R/tq_visualization.R R/transcript_models_build_helpers.R R/transcript_quantifier-class.R R/transcript_shape_profile-class.R R/tss_predictor.R R/txdb_handling.R R/type_checkers.R R/upstream_density_ratio.R R/zzz.R README.md inst/extdata/make_density_ratio_bw.R inst/extdata/make_multichrom_bw.R inst/extdata/make_test_files_single_strand.R inst/extdata/make_test_files_two_strands.R inst/extdata/test_transcript_filter.R man/add_data.Rd man/apply_bigwig_seqinfo.Rd man/apply_shape_profile.Rd man/assert_chromosome_exists.Rd man/cache_create_dir.Rd man/cache_defaults.Rd man/cache_get_dir.Rd man/cache_set_dir.Rd man/collect_tss_features.Rd man/covered_bases.Rd man/create_bins.Rd man/create_model_masks.Rd man/create_transcript_models.Rd man/download_txdb.Rd man/fit.Rd man/gene_abundance.Rd man/get_abundance.Rd man/get_data.Rd man/get_masks.Rd man/get_transcribed_regions.Rd man/get_transcripts.Rd man/get_tx_id.Rd man/group_trancript_models.Rd man/group_transcripts.Rd man/is_length_two_vector.Rd man/is_matrix_list.Rd man/is_strand_vector.Rd man/is_vector_list.Rd man/label_transcripts.Rd man/labeled_feature_set.Rd man/list_cached_txdb.Rd man/load_txdb.Rd man/locus_statistics.Rd man/locus_variance_explained.Rd man/mask_data.Rd man/mask_transcripts.Rd man/matrix_list_dim_equal.Rd man/model_agreement.Rd man/plot_model.Rd man/predict_inactive_transcripts.Rd man/predict_locus.Rd man/predict_transcripts.Rd man/reduce_transcript_models.Rd man/rescale_fixed_width_position.Rd man/save_txdb.Rd man/seqv.Rd man/set_datatrack_ylim.Rd man/show-transcript_quantifier-method.Rd man/split_path.Rd man/strip_loess.Rd man/sum_squares_grad.Rd man/sum_squares_lasso.Rd man/summarize_bigwig.Rd man/total_coverage.Rd man/transcript_abundance.Rd man/transcript_quantifier-class.Rd man/transcript_quantifier.Rd man/transcript_quantifier_valid.Rd man/transcript_shape_profile-class.Rd man/transcript_shape_profile.Rd man/tss_predictor.Rd man/tx_variance_explained.Rd man/upstream_polymerase_ratio.Rd man/view.Rd man/view_available_txdb.Rd man/window_regions.Rd tests/testthat.R tests/testthat/setup-linting.R tests/testthat/setup-model_fitting.R tests/testthat/teardown-caching.R tests/testthat/test-caching.R tests/testthat/test-linting.R tests/testthat/test-model_fitting.R tests/testthat/test-plotting.R tests/testthat/test-process_data.R tests/testthat/test-reduce_transcript_model.R tests/testthat/test-shape_profile.R tests/testthat/test-transcript_model.R tests/testthat/test-tss_prediction.R tests/testthat/test-type_checkers.R vignettes/introduction.Rmd