Files in tidybulk

Brings transcriptomics to the tidyverse

README.md R/methods.R R/cibersort.R R/utils-pipe.R R/utilities.R R/bibliography.R R/dplyr_methods.R R/data.R R/methods_SE.R R/tidybulk-package.R R/functions.R R/dictionary.R R/tidyr_methods.R R/validation.R inst/doc/manuscript_differential_transcript_abundance.R inst/doc/manuscript_transcriptional_signatures.Rmd inst/doc/comparison_with_base_R.Rmd inst/doc/manuscript_transcriptional_signatures.R inst/doc/manuscript_differential_transcript_abundance.Rmd inst/doc/comparison_with_base_R.R inst/doc/introduction.R inst/doc/introduction.Rmd build/tidybulk.pdf tests/testthat.R tests/testthat/test-bulk_methods.R tests/testthat/test-bulk_methods_SummarizedExperiment.R vignettes/manuscript_transcriptional_signatures.Rmd vignettes/comparison_with_base_R.Rmd vignettes/manuscript_differential_transcript_abundance.Rmd vignettes/introduction.Rmd man/check_if_duplicated_genes.Rd man/check_if_wrong_input.Rd man/get_x_y_annotation_columns.Rd man/add_attr.Rd man/check_if_counts_is_na.Rd man/breast_tcga_mini.Rd man/flybaseIDs.Rd man/add_scaled_counts_bulk.calcNormFactor.Rd man/se_mini.Rd man/se.Rd man/get_abundance_norm_if_exists.Rd man/keep_variable-methods.Rd man/counts.Rd man/tidyr-methods.Rd man/reexports.Rd man/test_gene_enrichment-methods.Rd man/identify_abundant-methods.Rd man/log10_reverse_trans.Rd man/create_tt_from_bam_sam_bulk.Rd man/aggregate_duplicated_transcripts_bulk.Rd man/impute_missing_abundance-methods.Rd man/prepend.Rd man/get_cell_type_proportions.Rd man/test_differential_abundance-methods.Rd man/get_sample_counts.Rd man/counts_ensembl.Rd man/get_reduced_dimensions_PCA_bulk.Rd man/get_differential_transcript_abundance_deseq2.Rd man/inner_join.Rd man/reduce_dimensions-methods.Rd man/scale_abundance-methods.Rd man/symbol_to_entrez.Rd man/run_llsr.Rd man/get_adjusted_counts_for_unwanted_variation_bulk.Rd man/aggregate_duplicates-methods.Rd man/remove_redundancy-methods.Rd man/distinct.Rd man/ifelse_pipe.Rd man/get_symbol_from_ensembl.Rd man/ensembl_symbol_mapping.Rd man/error_if_duplicated_genes.Rd man/cluster_elements-methods.Rd man/error_if_log_transformed.Rd man/rename.Rd man/describe_transcript.Rd man/summarise.Rd man/rotate_dimensions-methods.Rd man/parse_formula.Rd man/ensembl_to_symbol-methods.Rd man/error_if_counts_is_na.Rd man/fill_missing_abundance-methods.Rd man/fill_NA_using_formula.Rd man/group_by.Rd man/ifelse2_pipe.Rd man/get_bibliography-methods.Rd man/fill_NA_using_value.Rd man/get_sample_transcript.Rd man/get_reduced_dimensions_MDS_bulk.Rd man/get_clusters_kmeans_bulk.Rd man/rowwise.Rd man/get_sample.Rd man/get_transcript.Rd man/fill_NA_with_row_median.Rd man/get_sample_transcript_counts.Rd man/parse_formula_survival.Rd man/full_join.Rd man/get_reduced_dimensions_TSNE_bulk.Rd man/left_join.Rd man/pipe.Rd man/quo_names.Rd man/get_differential_transcript_abundance_bulk_voom.Rd man/counts_mini.Rd man/X_cibersort.Rd man/mutate.Rd man/remove_redundancy_elements_though_reduced_dimensions.Rd man/deconvolve_cellularity-methods.Rd man/vignette_manuscript_signature_tsne.Rd man/dplyr-methods.Rd man/get_scaled_counts_bulk.Rd man/get_clusters_SNN_bulk.Rd man/scale_design.Rd man/get_differential_transcript_abundance_bulk.Rd man/bind.Rd man/pivot_sample-methods.Rd man/test_gene_overrepresentation-methods.Rd man/get_elements_features_abundance.Rd man/vignette_manuscript_signature_boxplot.Rd man/add_class.Rd man/tidybulk_SAM_BAM-methods.Rd man/drop_class.Rd man/remove_redundancy_elements_through_correlation.Rd man/get_elements.Rd man/test_differential_cellularity-methods.Rd man/logit_trans.Rd man/drop_attr.Rd man/filter.Rd man/keep_variable_transcripts.Rd man/select_closest_pairs.Rd man/get_rotated_dimensions.Rd man/add_scaled_counts_bulk.get_low_expressed.Rd man/tidybulk-methods.Rd man/run_epic.Rd man/right_join.Rd man/pivot_transcript-methods.Rd man/error_if_wrong_input.Rd man/tidybulk_to_SummarizedExperiment.Rd man/create_tt_from_tibble_bulk.Rd man/adjust_abundance-methods.Rd man/test_differential_cellularity_.Rd man/as_matrix.Rd man/get_elements_features.Rd man/test_gene_enrichment_bulk_EGSEA.Rd man/vignette_manuscript_signature_tsne2.Rd man/keep_abundant-methods.Rd man/test_deseq2_df.Rd