Files in stemangiola/ttBulk
Brings transcriptomics to the tidyverse
.Rbuildignore
.coveralls.yml
.github/.gitignore
.github/workflows/rworkflows.yml
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/bibliography.R
R/cibersort.R
R/data.R
R/dictionary.R
R/dplyr_methods.R
R/functions.R
R/functions_SE.R
R/ggplot.R
R/glmmSeq.R
R/methods.R
R/methods_SE.R
R/tibble.R
R/tidySummarizedExperiment.R
R/tidybulk-package.R
R/tidyr_methods.R
R/utilities.R
R/utils-pipe.R
R/validation.R
R/zzz.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data/X_cibersort.rda
data/breast_tcga_mini_SE.rda
data/counts_ensembl.rda
data/ensembl_symbol_mapping.rda
data/flybaseIDs.rda
data/se.rda
data/se_mini.rda
data/tximeta_summarizeToGene_object.rda
data/vignette_manuscript_signature_boxplot.rda
data/vignette_manuscript_signature_tsne.rda
data/vignette_manuscript_signature_tsne2.rda
dev/.gitignore
dev/N52_workflow.R
dev/TCGA_processing_SE.R
dev/TCGA_processing_tibble.R
dev/benchmark/TCGA_workflow_standard.R
dev/benchmark/TCGA_workflow_ttBulk_for_comparison.R
dev/benchmark/pasilla_benchmark.pdf
dev/benchmark/pasilla_comparative_analyses.R
dev/benchmark/pasilla_workflow_standard.R
dev/benchmark/pasilla_workflow_ttBulk_for_comparison.R
dev/benchmark/stats_TCGA_standard.rds
dev/benchmark/stats_TCGA_ttBulk.rds
dev/benchmark/stats_pasilla_standard.rds
dev/benchmark/stats_pasilla_ttBulk.rds
dev/comparison_with_base_R.Rmd
dev/dplyr-master-methods.R
dev/format_GO.R
dev/manuscript_differential_transcript_abundance.Rmd
dev/manuscript_transcriptional_signatures.Rmd
dev/pasilla_workflow.R
dev/signature_workflow.R
dev/solve_complete_confounders.R
inst/CITATION
inst/NEWS.rd
inst/Thumbs.db
inst/logo.svg
inst/logo_source_no_outline.svg
man/X_cibersort.Rd
man/adjust_abundance-methods.Rd
man/aggregate_duplicates-methods.Rd
man/arrange-methods.Rd
man/as_SummarizedExperiment-methods.Rd
man/as_matrix.Rd
man/bind_rows.Rd
man/breast_tcga_mini_SE.Rd
man/check_if_counts_is_na.Rd
man/check_if_duplicated_genes.Rd
man/check_if_wrong_input.Rd
man/cluster_elements-methods.Rd
man/counts_ensembl.Rd
man/deconvolve_cellularity-methods.Rd
man/describe_transcript-methods.Rd
man/distinct-methods.Rd
man/dplyr-methods.Rd
man/ensembl_symbol_mapping.Rd
man/ensembl_to_symbol-methods.Rd
man/figures/SNN_plot-1.png
man/figures/logo.png
man/figures/new_SE_usage-01.png
man/figures/plot_cibersort-1.png
man/figures/plot_cluster-1.png
man/figures/plot_drop-1.png
man/figures/plot_drop2-1.png
man/figures/plot_mds-1.png
man/figures/plot_normalise-1.png
man/figures/plot_pca-1.png
man/figures/plot_rotate_1-1.png
man/figures/plot_rotate_2-1.png
man/figures/unnamed-chunk-11-1.png
man/figures/unnamed-chunk-12-1.png
man/figures/unnamed-chunk-13-1.png
man/figures/unnamed-chunk-14-1.png
man/figures/unnamed-chunk-16-1.png
man/figures/unnamed-chunk-17-1.png
man/figures/unnamed-chunk-19-1.png
man/fill_missing_abundance-methods.Rd
man/filter-methods.Rd
man/flybaseIDs.Rd
man/get_bibliography-methods.Rd
man/get_reduced_dimensions_UMAP_bulk.Rd
man/get_reduced_dimensions_UMAP_bulk_SE.Rd
man/group_by-methods.Rd
man/identify_abundant-methods.Rd
man/impute_missing_abundance-methods.Rd
man/join-methods.Rd
man/keep_abundant-methods.Rd
man/keep_variable-methods.Rd
man/log10_reverse_trans.Rd
man/logit_trans.Rd
man/mutate-methods.Rd
man/nest-methods.Rd
man/pipe.Rd
man/pivot_sample-methods.Rd
man/pivot_transcript-methods.Rd
man/quantile_normalise_abundance-methods.Rd
man/reduce_dimensions-methods.Rd
man/reexports.Rd
man/remove_redundancy-methods.Rd
man/rename-methods.Rd
man/resolve_complete_confounders_of_non_interest-methods.Rd
man/resolve_complete_confounders_of_non_interest.Rd
man/rotate_dimensions-methods.Rd
man/rowwise-methods.Rd
man/scale_abundance-methods.Rd
man/se.Rd
man/se_mini.Rd
man/summarise-methods.Rd
man/symbol_to_entrez.Rd
man/test_differential_abundance-methods.Rd
man/test_differential_cellularity-methods.Rd
man/test_gene_enrichment-methods.Rd
man/test_gene_overrepresentation-methods.Rd
man/test_gene_rank-methods.Rd
man/test_stratification_cellularity-methods.Rd
man/tidybulk-methods.Rd
man/tidybulk_SAM_BAM-methods.Rd
man/tximeta_summarizeToGene_object.Rd
man/vignette_manuscript_signature_boxplot.Rd
man/vignette_manuscript_signature_tsne.Rd
man/vignette_manuscript_signature_tsne2.Rd
tests/testthat.R
tests/testthat/test-bulk_methods.R
tests/testthat/test-bulk_methods_SummarizedExperiment.R
tests/testthat/test-tximeta_GRnges_IRanges.R
vignettes/.gitignore
vignettes/introduction.Rmd
