Files in stemangiola/ttBulk
Friendly tidy wrappers for facilitating transcriptional analyses

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/cibersort.R R/data.R R/functions_bulk.R R/methods.R R/utilities.R README.Rmd README.md
README_files/figure-gfm/SNN-1.png
README_files/figure-gfm/SNN_plot-1.png
README_files/figure-gfm/plot_cibersort-1.png
README_files/figure-gfm/plot_cluster-1.png
README_files/figure-gfm/plot_drop-1.png
README_files/figure-gfm/plot_drop2-1.png
README_files/figure-gfm/plot_mds-1.png
README_files/figure-gfm/plot_normalise-1.png
README_files/figure-gfm/plot_pca-1.png
README_files/figure-gfm/plot_rotate_1-1.png
README_files/figure-gfm/plot_rotate_2-1.png
README_files/figure-gfm/tsne-1.png
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README_files/figure-markdown_github/plot_cibersort-1.png
README_files/figure-markdown_github/plot_cluster-1.png
README_files/figure-markdown_github/plot_drop-1.png
README_files/figure-markdown_github/plot_drop2-1.png
README_files/figure-markdown_github/plot_mds-1.png
README_files/figure-markdown_github/plot_normalise-1.png
README_files/figure-markdown_github/plot_pca-1.png
README_files/figure-markdown_github/plot_rotate_1-1.png
README_files/figure-markdown_github/plot_rotate_2-1.png
codecov.yml
data/X_cibersort.rda
data/breast_tcga_mini.rda
data/counts.csv
data/counts.rda
data/counts_ensembl.rda
data/counts_mini.rda
data/ensembl_symbol_mapping.csv
data/ensembl_symbol_mapping.rda
doc/introduction.R doc/introduction.Rmd
doc/introduction.html
inst/Thumbs.db
inst/logo.png
inst/logo.svg
man/X_cibersort.Rd man/add_adjusted_counts_for_unwanted_variation_bulk.Rd man/add_attr.Rd man/add_cell_type_proportions.Rd man/add_class.Rd man/add_clusters_SNN_bulk.Rd man/add_clusters_kmeans_bulk.Rd man/add_differential_transcript_abundance_bulk.Rd man/add_normalised_counts_bulk.Rd man/add_normalised_counts_bulk.calcNormFactor.Rd man/add_normalised_counts_bulk.get_cpm.Rd man/add_normalised_counts_bulk.get_low_expressed.Rd man/add_reduced_dimensions_MDS_bulk.Rd man/add_reduced_dimensions_PCA_bulk.Rd man/add_reduced_dimensions_TSNE_bulk.Rd man/add_rotated_dimensions.Rd man/add_symbol_from_ensembl.Rd man/adjust_abundance.Rd man/aggregate_duplicated_transcripts_bulk.Rd man/aggregate_duplicates.Rd man/annotate_symbol.Rd man/as_matrix.Rd man/bind_rows.Rd man/breast_tcga_mini.Rd man/cluster_elements.Rd man/counts.Rd man/counts_ensembl.Rd man/counts_mini.Rd man/create_tt_from_bam_sam_bulk.Rd man/create_tt_from_tibble_bulk.Rd man/deconvolve_cellularity.Rd man/drop_class.Rd man/ensembl_symbol_mapping.Rd man/error_if_counts_is_na.Rd man/error_if_duplicated_genes.Rd man/error_if_log_transformed.Rd man/error_if_wrong_input.Rd man/filter_variable_transcripts.Rd man/get_abundance_norm_if_exists.Rd man/get_adjusted_counts_for_unwanted_variation_bulk.Rd man/get_cell_type_proportions.Rd man/get_clusters_SNN_bulk.Rd man/get_clusters_kmeans_bulk.Rd man/get_differential_transcript_abundance_bulk.Rd man/get_elements.Rd man/get_elements_features.Rd man/get_elements_features_abundance.Rd man/get_normalised_counts_bulk.Rd man/get_reduced_dimensions_MDS_bulk.Rd man/get_reduced_dimensions_PCA_bulk.Rd man/get_reduced_dimensions_TSNE_bulk.Rd man/get_rotated_dimensions.Rd man/get_sample_transcript.Rd man/get_sample_transcript_counts.Rd man/get_symbol_from_ensembl.Rd man/ifelse2_pipe.Rd man/ifelse_pipe.Rd man/left_join.Rd man/merged_ttBulk_object.Rd man/mutate.Rd man/parse_formula.Rd man/prepend.Rd man/reduce_dimensions.Rd man/remove_redundancy.Rd man/remove_redundancy_elements_though_reduced_dimensions.Rd man/remove_redundancy_elements_through_correlation.Rd man/rotate_dimensions.Rd man/scale_abundance.Rd man/scale_design.Rd man/select_closest_pairs.Rd man/test_differential_abundance.Rd man/ttBulk.Rd tests/testthat.R tests/testthat/test-bulk.R tests/testthat/test-bulk_methods.R
ttBulk.Rproj
vignettes/introduction.Rmd
vignettes/introduction_files/figure-html/SNN-1.png
vignettes/introduction_files/figure-html/plot_cibersort-1.png
vignettes/introduction_files/figure-html/plot_cluster-1.png
vignettes/introduction_files/figure-html/plot_mds-1.png
vignettes/introduction_files/figure-html/plot_normalise-1.png
vignettes/introduction_files/figure-html/plot_pca-1.png
vignettes/introduction_files/figure-html/plot_rotate_1-1.png
vignettes/introduction_files/figure-html/plot_rotate_2-1.png
vignettes/introduction_files/figure-html/tsne-1.png
stemangiola/ttBulk documentation built on Dec. 8, 2019, 4:27 p.m.