Files in zentnerlab/TSRexploreR

TSS and TSR Analysis

.Rbuildignore

.github/.gitignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/RcppExports.R R/TSRexplore.R R/TSRexploreR-package.R R/annotate.R R/association.R R/bam_processing.R R/convenience_methods.R R/correlation.R R/count_matrix.R R/data.R R/data_conditionals.R R/data_export.R R/data_import.R R/density_plots.R R/diff_exp_plots.R R/diff_expression.R R/dim_reduction.R R/dinucleotide.R R/gene_plots.R R/gene_tracks.R R/genomic_distribution.R R/getters.R R/heatmaps.R R/merge.R R/motif.R R/normalize.R R/package_imports.R R/params.R R/prepare_counts.R R/sequences.R R/shifting_plots.R R/softclip_analysis.R R/thresholding.R R/tsr_metrics.R R/tsr_plots.R R/tss_clustering.R R/tss_metrics.R R/tss_shifting.R R/utils-pipe.R README.md

_pkgdown.yml

data/TSSs.rda

data/TSSs_reduced.rda

docs/404.html

docs/LICENSE-text.html

docs/_config.yml

docs/articles/BAM_PROCESSING.html

docs/articles/BAM_PROCESSING_files/figure-html/unnamed-chunk-3-1.png

docs/articles/BAM_PROCESSING_files/figure-html/unnamed-chunk-4-1.png

docs/articles/BAM_PROCESSING_files/header-attrs-2.7/header-attrs.js

docs/articles/DATA_CONDITIONING.html

docs/articles/DATA_CONDITIONING_files/figure-html/unnamed-chunk-2-1.png

docs/articles/DATA_CONDITIONING_files/figure-html/unnamed-chunk-3-1.png

docs/articles/DATA_CONDITIONING_files/figure-html/unnamed-chunk-4-1.png

docs/articles/DATA_CONDITIONING_files/figure-html/unnamed-chunk-5-1.png

docs/articles/DATA_CONDITIONING_files/figure-html/unnamed-chunk-6-1.png

docs/articles/DATA_CONDITIONING_files/header-attrs-2.7/header-attrs.js

docs/articles/DIFF_FEATURES.html

docs/articles/DIFF_FEATURES_files/figure-html/unnamed-chunk-10-1.png

docs/articles/DIFF_FEATURES_files/figure-html/unnamed-chunk-11-1.png

docs/articles/DIFF_FEATURES_files/figure-html/unnamed-chunk-12-1.png

docs/articles/DIFF_FEATURES_files/figure-html/unnamed-chunk-3-1.png

docs/articles/DIFF_FEATURES_files/figure-html/unnamed-chunk-4-1.png

docs/articles/DIFF_FEATURES_files/figure-html/unnamed-chunk-8-1.png

docs/articles/DIFF_FEATURES_files/figure-html/unnamed-chunk-9-1.png

docs/articles/DIFF_FEATURES_files/header-attrs-2.7/header-attrs.js

docs/articles/FEATURE_SHIFT.html

docs/articles/FEATURE_SHIFT_files/figure-html/unnamed-chunk-4-1.png

docs/articles/FEATURE_SHIFT_files/figure-html/unnamed-chunk-5-1.png

docs/articles/FEATURE_SHIFT_files/figure-html/unnamed-chunk-7-1.png

docs/articles/FEATURE_SHIFT_files/figure-html/unnamed-chunk-8-1.png

docs/articles/FEATURE_SHIFT_files/header-attrs-2.7/header-attrs.js

docs/articles/STANDARD_ANALYSIS.html

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-10-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-11-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-12-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-13-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-14-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-19-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-20-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-21-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-22-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-23-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-24-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-25-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-5-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-7-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-8-1.png

docs/articles/STANDARD_ANALYSIS_files/figure-html/unnamed-chunk-9-1.png

docs/articles/STANDARD_ANALYSIS_files/header-attrs-2.7/header-attrs.js

docs/articles/index.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/G_correction.html

docs/reference/Rplot001.png

docs/reference/ShiftScores-function.html

docs/reference/TSSs.html

docs/reference/TSSs_reduced.html

docs/reference/annotate_features.html

docs/reference/apply_threshold.html

docs/reference/associate_with_tsr.html

docs/reference/common_params.html

docs/reference/condition_data.html

docs/reference/conditionals.html

docs/reference/differential_expression.html

docs/reference/dot-count_features.html

docs/reference/dot-count_matrix.html

docs/reference/dot-de_status.html

docs/reference/dot-out_of_bounds_index.html

docs/reference/dot-prepare_annotation.html

docs/reference/dot-prepare_assembly.html

docs/reference/export_for_enrichment.html

docs/reference/extract_counts-function.html

docs/reference/extract_de-function.html

docs/reference/extract_matrix-function.html

docs/reference/fit_de_model.html

docs/reference/format_counts.html

docs/reference/gene_tracks.html

docs/reference/get_annotation.html

docs/reference/get_assembly.html

docs/reference/get_counts.html

docs/reference/get_diff_model.html

docs/reference/get_diff_results.html

docs/reference/get_granges.html

docs/reference/get_sample_sheet.html

docs/reference/get_shifting_results.html

docs/reference/import_bams.html

docs/reference/index.html

docs/reference/mark_dominant.html

docs/reference/merge_samples.html

docs/reference/normalize_counts.html

docs/reference/ordering.html

docs/reference/pipe.html

docs/reference/plot_correlation.html

docs/reference/plot_density.html

docs/reference/plot_detected_features.html

docs/reference/plot_dinucleotide_frequencies.html

docs/reference/plot_genomic_distribution.html

docs/reference/plot_heatmap.html

docs/reference/plot_ma.html

docs/reference/plot_num_de.html

docs/reference/plot_reduction.html

docs/reference/plot_sequence_colormap.html

docs/reference/plot_sequence_logo.html

docs/reference/plot_shift_count.html

docs/reference/plot_shift_rank.html

docs/reference/plot_threshold_exploration.html

docs/reference/plot_tsr_metric.html

docs/reference/plot_volcano.html

docs/reference/preliminary_filter.html

docs/reference/quantiling.html

docs/reference/retrieve_seqs.html

docs/reference/set_slot-function.html

docs/reference/softclip_composition.html

docs/reference/softclip_histogram.html

docs/reference/tsr_experiment-generic.html

docs/reference/tsr_explorer-class.html

docs/reference/tsr_export.html

docs/reference/tsr_import.html

docs/reference/tsr_metrics.html

docs/reference/tss_aggregate.html

docs/reference/tss_clustering.html

docs/reference/tss_experiment-generic.html

docs/reference/tss_export.html

docs/reference/tss_import.html

docs/reference/tss_shift.html

documentation/BAM_PROCESSING.pdf documentation/DATA_CONDITIONING.pdf documentation/DIFF_FEATURES.pdf documentation/FEATURE_SHIFT.pdf documentation/STANDARD_ANALYSIS.pdf

inst/extdata/S288C.bam

inst/extdata/S288C.bam.bai

inst/extdata/S288C_Annotation.gtf

inst/extdata/S288C_Assembly.fasta

inst/extdata/S288C_TSRs.RDS

inst/extdata/S288C_TSSs.RDS

inst/extdata/yeast_RNAseq.RDS

inst/extdata/yeast_TSSs_total.RDS

inst/singularity/singularity-recipe

man/G_correction.Rd man/ShiftScores-function.Rd man/TSSs.Rd man/TSSs_reduced.Rd man/annotate_features.Rd man/apply_threshold.Rd man/associate_with_tsr.Rd man/common_params.Rd man/condition_data.Rd man/conditionals.Rd man/differential_expression.Rd man/dot-count_features.Rd man/dot-count_matrix.Rd man/dot-de_status.Rd man/dot-out_of_bounds_index.Rd man/dot-prepare_annotation.Rd man/dot-prepare_assembly.Rd man/export_for_enrichment.Rd man/extract_counts-function.Rd man/extract_de-function.Rd man/extract_matrix-function.Rd man/fit_de_model.Rd man/format_counts.Rd man/gene_tracks.Rd man/get_annotation.Rd man/get_assembly.Rd man/get_counts.Rd man/get_diff_model.Rd man/get_diff_results.Rd man/get_granges.Rd man/get_sample_sheet.Rd man/get_shifting_results.Rd man/import_bams.Rd man/mark_dominant.Rd man/merge_samples.Rd man/normalize_counts.Rd man/ordering.Rd man/pipe.Rd man/plot_correlation.Rd man/plot_density.Rd man/plot_detected_features.Rd man/plot_dinucleotide_frequencies.Rd man/plot_genomic_distribution.Rd man/plot_heatmap.Rd man/plot_ma.Rd man/plot_num_de.Rd man/plot_reduction.Rd man/plot_sequence_colormap.Rd man/plot_sequence_logo.Rd man/plot_shift_count.Rd man/plot_shift_rank.Rd man/plot_threshold_exploration.Rd man/plot_tsr_metric.Rd man/plot_volcano.Rd man/preliminary_filter.Rd man/quantiling.Rd man/retrieve_seqs.Rd man/set_slot-function.Rd man/softclip_composition.Rd man/softclip_histogram.Rd man/tsr_experiment-generic.Rd man/tsr_explorer-class.Rd man/tsr_export.Rd man/tsr_import.Rd man/tsr_metrics.Rd man/tss_aggregate.Rd man/tss_clustering.Rd man/tss_experiment-generic.Rd man/tss_export.Rd man/tss_import.Rd man/tss_shift.Rd

src/.gitignore

src/Makevars

src/Makevars.win

src/RcppExports.cpp

src/shiftscore.cpp

tests/testthat.R tests/testthat/setup.R tests/testthat/test-TSS_processing.R tests/testthat/test-bam_processing.R tests/testthat/test-correlation.R tests/testthat/test-density_plots.R tests/testthat/test-differential_features.R tests/testthat/test-genome.R tests/testthat/test-heatmap.R tests/testthat/test-ranges.R tests/testthat/test-sequence_related.R tests/testthat/test-shiftscore-cpp.R vignettes/BAM_PROCESSING.Rmd vignettes/DATA_CONDITIONING.Rmd vignettes/DIFF_FEATURES.Rmd vignettes/FEATURE_SHIFT.Rmd vignettes/STANDARD_ANALYSIS.Rmd

zentnerlab/TSRexploreR documentation built on Dec. 30, 2022, 10:27 p.m.