Files in TeamMacLean/atacr
Analysing Capture Seq Count Data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/atacr.R
R/differentials.R
R/figures.R
R/loading.R
R/methods.R
R/normalisation.R
R/sims.R
README-unnamed-chunk-2-1.png
README.Rmd
README.md
atacr.Rproj
data/athal_wt_counts.rda
data/sim_counts.rda
data/small_counts.rda
docs/atacr.html
docs/atacr_which.html
docs/differential_windows.html
docs/index.html
docs/loading.html
docs/normalisations.html
docs/summaries.html
docs/tutorial.Rmd
docs/tutorial.html
docs/tutorial_cache/html/__packages
docs/tutorial_cache/html/pca_plot_d5010f9ca43af72d0bc587807a7bf3d9.RData
docs/tutorial_cache/html/pca_plot_d5010f9ca43af72d0bc587807a7bf3d9.rdb
docs/tutorial_cache/html/pca_plot_d5010f9ca43af72d0bc587807a7bf3d9.rdx
docs/tutorial_cache/html/plot_plot_24f20174733d96dba5249a7d35c2c80c.RData
docs/tutorial_cache/html/plot_plot_24f20174733d96dba5249a7d35c2c80c.rdb
docs/tutorial_cache/html/plot_plot_24f20174733d96dba5249a7d35c2c80c.rdx
docs/tutorial_files/figure-html/coverage_threshold-1.png
docs/tutorial_files/figure-html/ma_plot-1.png
docs/tutorial_files/figure-html/pca_plot-1.png
docs/tutorial_files/figure-html/plot_plot-1.png
docs/tutorial_files/figure-html/unnamed-chunk-4-1.png
docs/tutorial_files/figure-html/unnamed-chunk-5-1.png
docs/tutorial_files/figure-html/unnamed-chunk-7-1.png
docs/tutorial_files/figure-html/unnamed-chunk-8-1.png
docs/tutorial_files/figure-html/unnamed-chunk-8-2.png
docs/tutorial_files/figure-html/unnamed-chunk-8-3.png
docs/tutorial_files/figure-html/unnamed-chunk-8-4.png
docs/tutorial_files/figure-html/unnamed-chunk-9-1.png
docs/tutorial_files/figure-html/unnamed-chunk-9-2.png
docs/tutorial_files/figure-html/unnamed-chunk-9-3.png
docs/tutorial_files/figure-html/unnamed-chunk-9-4.png
inst/extdata/ATAC102/alignedSorted.bam
inst/extdata/ATAC102/alignedSorted.bam.bai
inst/extdata/ATAC103/alignedSorted.bam
inst/extdata/ATAC103/alignedSorted.bam.bai
inst/extdata/ATAC202/alignedSorted.bam
inst/extdata/ATAC202/alignedSorted.bam.bai
inst/extdata/ATAC203/alignedSorted.bam
inst/extdata/ATAC203/alignedSorted.bam.bai
inst/extdata/ATAC302/alignedSorted.bam
inst/extdata/ATAC302/alignedSorted.bam.bai
inst/extdata/ATAC303/alignedSorted.bam
inst/extdata/ATAC303/alignedSorted.bam.bai
inst/extdata/bait_regions.gff
inst/extdata/tutorial_mappings.csv
man/Est.Depth.Rd
man/as.DGEList.Rd
man/as.data.frame.atacr.Rd
man/as.matrix.atacr.Rd
man/assay_matrix_to_df.Rd
man/athal_wt_counts.Rd
man/bootstrap_t.Rd
man/calc_quantiles.Rd
man/chromosome_coverage.Rd
man/control_window_normalise.Rd
man/control_window_normalise_internal.Rd
man/control_window_scaling_factors.Rd
man/count_windows_under_threshold.Rd
man/coverage_count_summary.Rd
man/coverage_summary.Rd
man/edgeR_exact.Rd
man/edgeR_multiclass.Rd
man/estimate_GoFs.Rd
man/estimate_bayes_factor.Rd
man/estimate_bayes_factor_multiclass.Rd
man/estimate_fdr.Rd
man/estimate_fdr_multiclass.Rd
man/extract_features_from_gff.Rd
man/find_controls_by_GoF.Rd
man/get_GoF_factors.Rd
man/get_bait_regions_from_gff.Rd
man/get_bait_regions_from_text.Rd
man/get_expected_values.Rd
man/get_t.Rd
man/gof.Rd
man/library_size_normalisation.Rd
man/library_size_normalisation_internal.Rd
man/library_size_scaling_factors.Rd
man/load_atac.Rd
man/load_rnaseq.Rd
man/ma_data.Rd
man/ma_plot.Rd
man/make_UpSetR.Rd
man/make_corrplot.Rd
man/make_counts.Rd
man/make_csaw_params.Rd
man/make_params.Rd
man/make_scanBamParam.Rd
man/make_tutorial_data.Rd
man/median_virtual_experiment.Rd
man/normalise_by_window_width.Rd
man/observed_expected_bins.Rd
man/plot.atacr.Rd
man/plot_GoF.Rd
man/plot_count_by_chromosome.Rd
man/plot_counts.Rd
man/print.atacr.Rd
man/qqarb.Rd
man/read_experiment_info.Rd
man/sample_correlation_plot.Rd
man/sample_kmeans_cluster.Rd
man/sample_pca_plot.Rd
man/scale_factor_normalise.Rd
man/select_data.Rd
man/sim_counts.Rd
man/simulate_counts.Rd
man/small_counts.Rd
man/summary.atacr.Rd
man/target_count_coverage.Rd
man/target_count_summary.Rd
man/text_to_gff.Rd
man/treatments.Rd
man/view_gene.Rd
man/windows_below_coverage_threshold_plot.Rd
tests/testthat.R
tests/testthat/a1_smallSorted.bam
tests/testthat/a1_smallSorted.bam.bai
tests/testthat/a2_smallSorted.bam
tests/testthat/a2_smallSorted.bam.bai
tests/testthat/b1_smallSorted.bam
tests/testthat/b1_smallSorted.bam.bai
tests/testthat/b2_smallSorted.bam
tests/testthat/b2_smallSorted.bam.bai
tests/testthat/bait_genes.gff
tests/testthat/control_windows.txt
tests/testthat/helper-functions.R
tests/testthat/individual_bait_regions.gff
tests/testthat/individual_bait_regions.txt
tests/testthat/sample_treatment_bam_mappings_for_test.csv
tests/testthat/test_atacr.R
tests/testthat/test_differentials.R
tests/testthat/test_loading.R
tests/testthat/test_methods.R
tests/testthat/test_normalisation.R
vignettes/atacr.Rmd
vignettes/atacr_which.Rmd
vignettes/differential_windows.Rmd
vignettes/loading.Rmd
vignettes/normalisations.Rmd
vignettes/summaries.Rmd
