Files in stemangiola/tidybulk

Brings transcriptomics to the tidyverse

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 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/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 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/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/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/introduction.Rmd