Files in insightsengineering/hermes

Preprocessing, analyzing, and reporting of RNA-seq data

.github/CONTRIBUTING.md .github/pull_request_template.md NEWS.md R/GeneSpec-class.R R/HermesData-class.R R/HermesData-methods.R R/HermesData-validate.R R/argument_convention.R R/assertthat.R R/calc_cor.R R/checkmate.R R/connections.R R/data.R R/differential.R R/dplyr_compatibility.R R/draw_barplot.R R/draw_boxplot.R R/draw_heatmap.R R/draw_scatterplot.R R/graphs.R R/join_cdisc.R R/normalization.R R/package.R R/pca.R R/pca_cor_samplevar.R R/quality.R R/top_genes.R R/utils.R README.Rmd README.md data-raw/create_expression_set.R data-raw/create_hermes_data.R data-raw/create_multi_assay_experiment.R data-raw/create_summarized_experiment.R design/design_HermesData.Rmd design/design_all_plots.Rmd design/design_annotate_igis.Rmd design/design_biomart.Rmd design/design_classes.Rmd design/design_corr_pca.Rmd design/design_diff_expression.Rmd design/design_draw_boxplot.Rmd design/design_draw_filter_barplot.Rmd design/design_draw_libsize_densities.Rmd design/design_draw_libsize_hist.Rmd design/design_draw_libsize_qq.Rmd design/design_draw_nonzero_boxplot.Rmd design/design_flag_tech_failure.Rmd design/design_heatmap.Rmd design/design_heatmap_norm_counts.Rmd design/design_join_cdisc.Rmd design/design_mapping_args.Rmd design/design_normalization.Rmd design/design_pca_corr_original.Rmd design/design_pca_filter.Rmd design/design_quality_control.Rmd design/design_replace_df_explicit_na_function.Rmd design/design_show.Rmd design/design_summary.Rmd design/design_top_genes.Rmd design/design_transformation.Rmd inst/rmarkdown/templates/qc_report/skeleton/skeleton.Rmd man/GeneSpec.Rd man/HermesData-class.Rd man/all_na.Rd man/annotation.Rd man/assertion_arguments.Rd man/assertions.Rd man/calc_cor.Rd man/calc_pca.Rd man/cat_with_newline.Rd man/cbind.Rd man/check_proportion.Rd man/colMeanZscores.Rd man/colPrinComp1.Rd man/col_data_with_genes.Rd man/connect_biomart.Rd man/control_normalize.Rd man/control_quality.Rd man/correlate.Rd man/counts.Rd man/cut_quantile.Rd man/df_cols_to_factor.Rd man/diff_expression.Rd man/draw_barplot.Rd man/draw_boxplot.Rd man/draw_genes_barplot.Rd man/draw_heatmap.Rd man/draw_libsize_densities.Rd man/draw_libsize_hist.Rd man/draw_libsize_qq.Rd man/draw_nonzero_boxplot.Rd man/draw_scatterplot.Rd man/expression_set.Rd man/extra_data_names.Rd man/filter.Rd man/gene_spec.Rd man/genes.Rd man/h_all_duplicated.Rd man/h_df_factors_with_explicit_na.Rd man/h_diff_expr_deseq2.Rd man/h_diff_expr_voom.Rd man/h_ensembl_to_entrez_ids.Rd man/h_get_annotation_biomart.Rd man/h_get_granges_by_id.Rd man/h_get_size_biomart.Rd man/h_has_req_annotations.Rd man/h_map_pos.Rd man/h_parens.Rd man/h_pca_df_r2_matrix.Rd man/h_pca_var_rsquared.Rd man/h_short_list.Rd man/h_strip_prefix.Rd man/h_unique_labels.Rd man/hermes-package.Rd man/hermes_data.Rd man/inner_join_cdisc.Rd man/isEmpty.Rd man/lapply.Rd man/metadata.Rd man/multi_assay_experiment.Rd man/normalize.Rd man/pca_cor_samplevar.Rd man/pipe.Rd man/plot_all.Rd man/prefix.Rd man/quality_flags.Rd man/query.Rd man/rbind.Rd man/rename.Rd man/samples.Rd man/set_tech_failure.Rd man/show.Rd man/subset.Rd man/summarized_experiment.Rd man/summary.Rd man/top_genes.Rd man/validate.Rd man/wrap_in_mae.Rd tests/test_dplyr_compatibility.R tests/testthat.R tests/testthat/_snaps/draw_barplot.md tests/testthat/_snaps/draw_boxplot.md tests/testthat/_snaps/graphs.md tests/testthat/helper-data_funs.R tests/testthat/test-GeneSpec-class.R tests/testthat/test-HermesData-class.R tests/testthat/test-HermesData-methods.R tests/testthat/test-HermesData-validate.R tests/testthat/test-assertthat.R tests/testthat/test-calc_cor.R tests/testthat/test-checkmate.R tests/testthat/test-connections.R tests/testthat/test-data.R tests/testthat/test-differential.R tests/testthat/test-draw_barplot.R tests/testthat/test-draw_boxplot.R tests/testthat/test-draw_heatmap.R tests/testthat/test-draw_scatterplot.R tests/testthat/test-graphs.R tests/testthat/test-join_cdisc.R tests/testthat/test-normalization.R tests/testthat/test-pca.R tests/testthat/test-pca_cor_samplevar.R tests/testthat/test-quality.R tests/testthat/test-top_genes.R tests/testthat/test-utils.R tests/testthat/test.R vignettes/hermes.Rmd