Files in vari-bbc/bbcRNA
Bulk RNA-seq workflow for VAI BBC
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/AllClasses.R
R/AllGenerics.R
R/BbcEdgeR_manip_methods.R
R/BbcSE_manip_methods.R
R/aln_rates.R
R/bbcRNA.R
R/data_input.R
R/data_output.R
R/deseq2_methods.R
R/edger_methods.R
R/gsea.R
R/misc.R
R/row_data_methods.R
README.Rmd
README.md
_pkgdown.yml
bbcRNA.Rproj
codecov.yml
docs/404.html
docs/LICENSE-text.html
docs/_config.yml
docs/articles/index.html
docs/articles/rnaseq_from_star.html
docs/articles/rnaseq_from_star_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/rnaseq_from_star_files/anchor-sections-1.0/anchor-sections.css
docs/articles/rnaseq_from_star_files/anchor-sections-1.0/anchor-sections.js
docs/articles/rnaseq_from_star_files/figure-html/find_degs-1.png
docs/articles/rnaseq_from_star_files/figure-html/heatmap-1.png
docs/articles/rnaseq_from_star_files/figure-html/heatmap-2.png
docs/articles/rnaseq_from_star_files/figure-html/plot_Hgsea-1.png
docs/articles/rnaseq_from_star_files/figure-html/plot_hyper_kegg-1.png
docs/articles/rnaseq_from_star_files/figure-html/plot_kegggsea-1.png
docs/articles/rnaseq_from_star_files/figure-html/plot_kegggsea-2.png
docs/articles/rnaseq_from_star_files/figure-html/plot_mapping-1.png
docs/articles/rnaseq_from_star_files/figure-html/plot_mapping-2.png
docs/articles/rnaseq_from_star_files/figure-html/plot_pca-1.png
docs/articles/rnaseq_from_star_files/figure-html/plot_pca-2.png
docs/articles/rnaseq_from_star_files/figure-html/unnamed-chunk-3-1.png
docs/articles/rnaseq_from_star_files/figure-html/unnamed-chunk-3-2.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/BbcEdgeR-class.html
docs/reference/BbcEdgeR.html
docs/reference/BbcSE-class.html
docs/reference/BbcSE.html
docs/reference/Rplot001.png
docs/reference/aln_metrics-set.html
docs/reference/aln_metrics.html
docs/reference/aln_rates-set.html
docs/reference/aln_rates.html
docs/reference/batch_correct_norm_cts.html
docs/reference/bbcRNA.html
docs/reference/cbind-BbcSE-method.html
docs/reference/de_results-set.html
docs/reference/de_results.html
docs/reference/deseq2.html
docs/reference/dgelist-set.html
docs/reference/dgelist.html
docs/reference/edger-set.html
docs/reference/edger.html
docs/reference/ens2entrez.html
docs/reference/ens2sym.html
docs/reference/findDEGs.html
docs/reference/find_missing_in_gseaResult.html
docs/reference/get_de_table.html
docs/reference/index.html
docs/reference/lists_to_edger_contrasts.html
docs/reference/makeDGEList.html
docs/reference/norm_cts-set.html
docs/reference/norm_cts.html
docs/reference/normalize_counts.html
docs/reference/plot_PCA.html
docs/reference/plot_aln_metrics.html
docs/reference/plot_aln_rates.html
docs/reference/plot_heatmap.html
docs/reference/plot_pval_distrib.html
docs/reference/plot_volcano.html
docs/reference/prep_clusterprofiler_genelist.html
docs/reference/rbind-BbcSE-method.html
docs/reference/read_col_meta.html
docs/reference/read_star_aln_metrics.html
docs/reference/read_star_map_rates.html
docs/reference/run_gsea.html
docs/reference/run_hypergeometric.html
docs/reference/searchBM.html
docs/reference/shorten_desc.html
docs/reference/show-BbcSE-method.html
docs/reference/star_to_mat.html
docs/reference/sub-BbcSE-ANY-ANY-ANY-method.html
docs/reference/subset-BbcSE-ANY-ANY-BbcSE-method.html
inst/extdata/tcell/SRR7240735_1_trimmed_Log.final.out
inst/extdata/tcell/SRR7240735_1_trimmed_ReadsPerGene.out.tab.gz
inst/extdata/tcell/SRR7240736_1_trimmed_Log.final.out
inst/extdata/tcell/SRR7240736_1_trimmed_ReadsPerGene.out.tab.gz
inst/extdata/tcell/SRR7240737_1_trimmed_Log.final.out
inst/extdata/tcell/SRR7240737_1_trimmed_ReadsPerGene.out.tab.gz
inst/extdata/tcell/SRR7240738_1_trimmed_Log.final.out
inst/extdata/tcell/SRR7240738_1_trimmed_ReadsPerGene.out.tab.gz
inst/extdata/tcell/SRR7240739_1_trimmed_Log.final.out
inst/extdata/tcell/SRR7240739_1_trimmed_ReadsPerGene.out.tab.gz
inst/extdata/tcell/SRR7240740_1_trimmed_Log.final.out
inst/extdata/tcell/SRR7240740_1_trimmed_ReadsPerGene.out.tab.gz
inst/extdata/tcell/SRR7240741_1_trimmed_Log.final.out
inst/extdata/tcell/SRR7240741_1_trimmed_ReadsPerGene.out.tab.gz
inst/extdata/tcell/SRR7240742_1_trimmed_Log.final.out
inst/extdata/tcell/SRR7240742_1_trimmed_ReadsPerGene.out.tab.gz
inst/extdata/tcell/meta.txt
man/BbcEdgeR-class.Rd
man/BbcEdgeR.Rd
man/BbcSE-class.Rd
man/BbcSE.Rd
man/aln_metrics-set.Rd
man/aln_metrics.Rd
man/batch_correct_norm_cts.Rd
man/bbcRNA.Rd
man/cbind-BbcSE-method.Rd
man/de_results-set.Rd
man/de_results.Rd
man/deseq2.Rd
man/dgelist-set.Rd
man/dgelist.Rd
man/edger-set.Rd
man/edger.Rd
man/ens2entrez.Rd
man/ens2sym.Rd
man/findDEGs.Rd
man/find_missing_in_gseaResult.Rd
man/get_de_table.Rd
man/lists_to_edger_contrasts.Rd
man/makeDGEList.Rd
man/norm_cts-set.Rd
man/norm_cts.Rd
man/normalize_counts.Rd
man/plot_PCA.Rd
man/plot_aln_metrics.Rd
man/plot_heatmap.Rd
man/plot_pval_distrib.Rd
man/plot_volcano.Rd
man/prep_clusterprofiler_genelist.Rd
man/rbind-BbcSE-method.Rd
man/read_col_meta.Rd
man/read_star_aln_metrics.Rd
man/run_gsea.Rd
man/run_hypergeometric.Rd
man/searchBM.Rd
man/shorten_desc.Rd
man/show-BbcSE-method.Rd
man/star_to_mat.Rd
man/sub-BbcSE-ANY-ANY-ANY-method.Rd
man/subset-BbcSE-ANY-ANY-BbcSE-method.Rd
tests/testthat.R
tests/testthat/setup.R
tests/testthat/test-BbcSE-manip.R
tests/testthat/test-data-output.R
tests/testthat/test-data_input.R
tests/testthat/test-edger.R
tests/testthat/test-geneset_enrichment.R
tests/testthat/test-rowData-methods.R
tests/testthat/test-visualization_funcs.R
vignettes/.gitignore
vignettes/rnaseq_from_star.Rmd
