Files in insightsengineering/hermes
Preprocessing, analyzing, and reporting of RNA-seq data
.Rbuildignore
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/bug.yml
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/feature.yml
.github/ISSUE_TEMPLATE/question.yml
.github/ISSUE_TEMPLATE/release.yaml
.github/pull_request_template.md
.github/workflows/check.yaml
.github/workflows/docs.yaml
.github/workflows/post-release.yaml
.github/workflows/release.yaml
.gitignore
.gitlab-ci.yml
.lintr
.pre-commit-config.yaml
DESCRIPTION
NAMESPACE
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
_pkgdown.yml
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
data-raw/summarized_experiment_colData.csv
data-raw/summarized_experiment_counts.csv
data-raw/summarized_experiment_rowData.csv
data/expression_set.rda
data/hermes_data.rda
data/multi_assay_experiment.rda
data/summarized_experiment.rda
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
hermes.Rproj
inst/REFERENCES.bib
inst/WORDLIST
inst/rmarkdown/templates/qc_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/qc_report/template.yaml
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/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-soft-deprecated.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/figures/logo.png
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
staged_dependencies.yaml
tests/test_dplyr_compatibility.R
tests/testthat.R
tests/testthat/_snaps/.gitignore
tests/testthat/_snaps/calc_cor/autoplot-for-hermesdatacor-with-custom-options.svg
tests/testthat/_snaps/calc_cor/autoplot-for-hermesdatacor-with-default-options.svg
tests/testthat/_snaps/differential/autoplot-for-hermesdatadiffexpr-with-default-options.svg
tests/testthat/_snaps/draw_barplot/draw-barplot-with-duplicate-labels.svg
tests/testthat/_snaps/draw_boxplot/draw-boxplot-with-duplicate-labels.svg
tests/testthat/_snaps/draw_heatmap/draw-heatmap-with-one-col-data-annotation.svg
tests/testthat/_snaps/draw_scatterplot/draw-scatterplot-with-duplicate-labels.svg
tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg
tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg
tests/testthat/_snaps/graphs/draw-libsize-densities-with-default-log.svg
tests/testthat/_snaps/graphs/draw-libsize-hist-with-10-blue-bins.svg
tests/testthat/_snaps/graphs/draw-libsize-qq-with-blue-solid-lines.svg
tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg
tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg
tests/testthat/_snaps/top_genes/autoplot-for-hermesdatatopgenes-with-custom-options.svg
tests/testthat/_snaps/top_genes/autoplot-for-hermesdatatopgenes-with-default-options.svg
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
tests/unit_testing_results.rds
vignettes/hermes.Rmd
vignettes/rmd_template_selection.png
