Files in tidybulk
Brings transcriptomics to the tidyverse
_pkgdown.yml
README.md
NAMESPACE
DESCRIPTION
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/Thumbs.db
inst/NEWS.rd
inst/logo.png
inst/logo_source_no_outline.svg
inst/logo.svg
inst/doc/manuscript_differential_transcript_abundance.R
inst/doc/manuscript_differential_transcript_abundance.html
inst/doc/manuscript_transcriptional_signatures.Rmd
inst/doc/comparison_with_base_R.html
inst/doc/comparison_with_base_R.Rmd
inst/doc/manuscript_transcriptional_signatures.R
inst/doc/manuscript_differential_transcript_abundance.Rmd
inst/doc/manuscript_transcriptional_signatures.html
inst/doc/introduction.html
inst/doc/comparison_with_base_R.R
inst/doc/introduction.R
inst/doc/introduction.Rmd
build/vignette.rds
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
data/counts_ensembl.rda
data/se_mini.rda
data/se.rda
data/ensembl_symbol_mapping.rda
data/vignette_manuscript_signature_tsne2.rda
data/flybaseIDs.rda
data/vignette_manuscript_signature_boxplot.rda
data/counts.rda
data/counts_mini.rda
data/test_deseq2_df.rda
data/X_cibersort.rda
data/vignette_manuscript_signature_tsne.rda
data/breast_tcga_mini.rda
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
man/figures/plot_mds-1.png
man/figures/plot_pca-1.png
man/figures/plot_rotate_1-1.png
man/figures/plot_drop2-1.png
man/figures/plot_drop-1.png
man/figures/SNN_plot-1.png
man/figures/unnamed-chunk-11-1.png
man/figures/plot_rotate_2-1.png
man/figures/plot_cluster-1.png
man/figures/plot_normalise-1.png
man/figures/plot_cibersort-1.png
