Files in CshlSiepelLab/DENR
Deconvolution of Expression for Nascent RNA Sequencing Data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE.md
NAMESPACE
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
codecov.yml
inst/extdata/conv_onelayer_61aa9200.hdf5
inst/extdata/conv_onelayer_61aa9200_input_info.yaml
inst/extdata/hsapiens_gene_ensembl_96_txdb_test
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_double_strand.txdb
inst/extdata/test_double_strand_minus.bw
inst/extdata/test_double_strand_plus.bw
inst/extdata/test_double_strands_minus.bw
inst/extdata/test_double_strands_plus.bw
inst/extdata/test_multichrom.bw
inst/extdata/test_multichrom.wig
inst/extdata/test_single_strand.bw
inst/extdata/test_single_strand.txdb
inst/extdata/test_transcript_filter.R
inst/extdata/test_transcript_filter.txdb
inst/extdata/test_transcript_filter_1_1000.bw
inst/extdata/test_transcript_filter_301_500.bw
inst/extdata/test_upr.txdb
inst/extdata/test_upr_minus.bw
inst/extdata/test_upr_plus.bw
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/figures/optimization.png
man/figures/transcript_model_creation.png
man/figures/upstream_polymerase_ratio.png
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/.gitignore
vignettes/introduction.Rmd
