Files in Sage-Bionetworks/sageseqr
Identify differentially expressed genes counts data
.DS_Store
.Rbuildignore
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/functions.R
R/globals.R
R/visualization-functions.R
README.md
_pkgdown.yml
config.yml
inst/_targets.R
inst/sageseqr-report.Rmd
man/association_statistic_for_factors.Rd
man/association_statistics_for_both.Rd
man/biomart_obj.Rd
man/biomart_stats.Rd
man/boxplot_vars.Rd
man/build_formula.Rd
man/check_mismatch.Rd
man/clean_covariates.Rd
man/coerce_continuous.Rd
man/coerce_factors.Rd
man/collapse_duplicate_hgnc_symbol.Rd
man/complete_path.Rd
man/compute_residuals.Rd
man/conditional_plot_sexcheck.Rd
man/convert_geneids.Rd
man/correlate_and_plot.Rd
man/cqn.Rd
man/differential_expression.Rd
man/dropped_genes.Rd
man/filter_genes.Rd
man/get_association_statistics.Rd
man/get_biomart.Rd
man/get_data.Rd
man/gtf_stats.Rd
man/identify_outliers.Rd
man/parse_counts.Rd
man/plot_coexpression.Rd
man/plot_pcs_with_covariates.Rd
man/plot_sexcheck.Rd
man/plot_sexcheck_pca.Rd
man/plot_volcano.Rd
man/prepare_results.Rd
man/provenance_helper.Rd
man/reexports.Rd
man/run_pca.Rd
man/run_pca_and_plot_correlations.Rd
man/simple_filter.Rd
man/start_de.Rd
man/stepwise_regression.Rd
man/store_results.Rd
man/summarize_biotypes.Rd
man/threshold_fdr.Rd
man/wrap_de.Rd
sageseqr-report.Rmd
sageseqr.Rproj
tests/testthat.R
tests/testthat/test-boxplot_vars.R
tests/testthat/test-build_formula.R
tests/testthat/test-check_mismatch.R
tests/testthat/test-clean_covariates.R
tests/testthat/test-compute_residuals.R
tests/testthat/test-convert_geneids.R
tests/testthat/test-differential_expression.R
tests/testthat/test-filter_genes.R
tests/testthat/test-parse_counts.R
tests/testthat/test-plot_sexcheck.R
tests/testthat/test-plot_sexcheck_pca.R
tests/testthat/test-stepwise_regression.R
vignettes/customize-config.Rmd
vignettes/run-the-plan.Rmd
vignettes/sagseqr-alpha-steps.Rmd
