Files in TeamMacLean/atacr
Analysing Capture Seq Count Data

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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
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docs/tutorial_cache/html/plot_plot_24f20174733d96dba5249a7d35c2c80c.RData
docs/tutorial_cache/html/plot_plot_24f20174733d96dba5249a7d35c2c80c.rdb
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docs/tutorial_files/figure-html/ma_plot-1.png
docs/tutorial_files/figure-html/pca_plot-1.png
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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
TeamMacLean/atacr documentation built on June 11, 2018, 7:15 p.m.