Files in xiayh17/RNAseqStat

A Pipeline to Process RNAseq Data

LICENSE.md R/data.R R/deg_DEseq2.R R/deg_edgeR.R R/deg_limma.R R/deg_run.R R/enhance_barplot.R R/enhance_build_Anno.R R/enhance_enrichGO.R R/enhance_enricher_internal.R R/enhance_get_GO_data.R R/enhance_gseplot.R R/enhance_heatmap.R R/enhance_volcano.R R/enrich_go.R R/enrich_gsekegg.R R/enrich_run.R R/erich_kegg.R R/globals.R R/pre_check.R R/runAll.R R/utils-pipe.R R/utils.R README.Rmd README.md data-raw/counts_input.R dev/ci.R dev/example_output/1-pre_check_all_samples_PCA_by_type.pdf dev/example_output/1-pre_check_cor_all.pdf dev/example_output/1-pre_check_cor_top500.pdf dev/example_output/1-pre_check_heatmap_top1000_sd.pdf dev/example_output/2-DEG_DEseq2_RAWvsNORM.pdf dev/example_output/2-DEG_DEseq2_qc_dispersions.pdf dev/example_output/2-DEG_DEseq2_top100_heatmap.pdf dev/example_output/2-DEG_DEseq2_volcano.pdf dev/example_output/2-DEG_edgeR_top100_heatmap.pdf dev/example_output/2-DEG_edgeR_volcano.pdf dev/example_output/2-DEG_limma_top100_heatmap.pdf dev/example_output/2-DEG_limma_volcano.pdf dev/example_output/3-EnrichGO_barplot-gene_Down_GO_enrichment.pdf dev/example_output/3-EnrichGO_barplot-gene_Up_GO_enrichment.pdf dev/example_output/3-EnrichGO_barplot-gene_diff_GO_enrichment.pdf dev/example_output/4-EnrichKEGG_up_and_down_KEGG.pdf dev/example_output/5-EnrichgseKEGG_gseKEGG_barplot.pdf dev/example_output/5-EnrichgseKEGG_gseKEGG_down_gseplot.pdf dev/example_output/5-EnrichgseKEGG_gseKEGG_up_gseplot.pdf dev/git.R dev/license.R dev/load.R dev/readme.R dev/test_GO.R dev/theme.R dev/usepackages.R man/DEG_container.Rd man/DEG_df.Rd man/barplot_base.Rd man/barplot_base2.Rd man/counts_input.Rd man/cut_much.Rd man/deg_DESeq2.Rd man/deg_edgeR.Rd man/deg_limma.Rd man/deg_run.Rd man/enhance_barplot.Rd man/enhance_enrichGO.Rd man/enhance_enricher_internal.Rd man/enhance_gseplot.Rd man/enhance_heatmap.Rd man/enhance_volcano.Rd man/enrichGO_run.Rd man/enrichKEGG_run.Rd man/enrich_go.Rd man/enrich_gsekegg.Rd man/enrich_kegg.Rd man/enrichgesKEGG_run.Rd man/geskegg_barplot.Rd man/go_res.Rd man/group_list.Rd man/kegg_barplot.Rd man/pre_check.Rd man/reexports.Rd man/runAll.Rd man/run_DESeq2.Rd man/run_edgeR.Rd man/run_limma.Rd man/top_deg.Rd tests/testthat.R tests/testthat/test-deg_DESeq2.R tests/testthat/test-pre_check.R vignettes/Check_your_data.Rmd vignettes/DEG_analysis.Rmd vignettes/RNASeq_analysis.Rmd vignettes/go.Rmd vignettes/gseKegg.Rmd vignettes/kegg.Rmd vignettes/tools_groupDEG.Rmd vignettes/tools_topDEG.Rmd vignettes/visualization_deg_heatmap.Rmd vignettes/visualization_deg_volcano.Rmd vignettes/visualization_go_barplot.Rmd vignettes/visualization_gsekegg_barplot.Rmd vignettes/visualization_gseplot.Rmd vignettes/visualization_kegg_barplot.Rmd