Files in Tong-Chen/YSX
For Yishengxin Training
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
Makefile
NAMESPACE
R/.history
R/.utilities.R.swp
R/1.R
R/WGCNA.R
R/enrich.R
R/flowerplot.R
R/pca.R
R/plot.R
R/singlecell.R
R/sp_EulerDiagrams.R
R/sp_barplot.R
R/sp_barplot.r
R/sp_boxplot.R
R/sp_corrplot.R
R/sp_dendrogram.R
R/sp_enrichment.R
R/sp_hclust.R
R/sp_histogram.R
R/sp_inflectionpoint.R
R/sp_lines.R
R/sp_lines.r
R/sp_manhattan2.R
R/sp_pca.R
R/sp_pcoa.R
R/sp_pheatmap.R
R/sp_raincloud.R
R/sp_scatter.R
R/sp_tree.R
R/sp_upsetView.R
R/sp_vennDiagram.R
R/sp_vennDiagram2.R
R/sp_vennDiagram3.R
R/sp_volcano.R
R/transcriptome.R
R/utilities.R
R/waterfalls.R
R/zzz.R
README.md
YSX.Rproj
alpha_metadata.txt
asv_compaund_pearson_cor.txt
build
build.r
demo/Bugbase/metadata.txt
demo/Bugbase/otutab.txt
demo/DirectCorrelation/DirectCorrelation.txt
demo/FAPROTAX/metadata.txt
demo/FAPROTAX/otutab_rare.txt
demo/FAPROTAX/taxonomy2.txt
demo/bar/exprTable.txt
demo/boxplot/alpha.txt
demo/boxplot/boxplot1.txt
demo/boxplot/boxplot2.txt
demo/boxplot/boxplot2metadata.txt
demo/boxplot/boxplot_singlecell.txt
demo/boxplot/boxplot_singlecell2.txt
demo/boxplot/metadata.txt
demo/cpcoa/cpcoa.txt
demo/cpcoa/cpcoaphenodata.txt
demo/enrichment/goeast.enrich.txt
demo/extractFasta/Human.fa
demo/extractFasta/Human.id.txt
demo/gene_id/celegans_gene_ensembl.txt
demo/gene_id/dmelanogaster_gene_ensembl.txt
demo/gene_id/hsapiens_gene_ensembl.txt
demo/gene_id/mmusculus_gene_ensembl.txt
demo/gene_id/ptroglodytes_gene_ensembl.txt
demo/gene_id/rnorvegicus_gene_ensembl.txt
demo/gene_id/tguttata_gene_ensembl.txt
demo/histogram/histogram_demo2.txt
demo/histogram/histogram_demo2.txt.histogram.r
demo/histogram/histogram_demo3.txt
demo/lefse/LEfSe2.txt
demo/limma/Microarray_compare.tsv
demo/limma/Microarray_metadata.tsv
demo/limma/Microarray_normalzied_log2.txt
demo/limma/ehbio_trans.Count_matrix.txt
demo/limma/sampleFile2.txt
demo/line/rare.txt
demo/pca/pca.txt
demo/pca/pca.txt.pca.pc_variance.xls
demo/pca/pca.txt.pca.pcs.xls
demo/pca/pca.txt.pca.pdf
demo/pca/pca.txt.pca.r
demo/pca/pca.txt.pca.weights.xls
demo/pca/pcaphenodata_.txt
demo/pcoa/pcoa.txt
demo/pcoa/pcoaphenodata.txt
demo/scatter/scatter3.txt
demo/scatter/scatter_demo2.txt
demo/transeq/filtered_test.fa
demo/transeq/nucleotide.fa
demo/upsetview/upset.txt
demo/upsetview/upsetview.data
demo/venn/venn_demo1.txt
demo/volcano/volcano.txt
demo/volcano/volcano2.txt
demo/volcano/volcano4.txt
demo/wgcna/LiverFemaleClean.txt
demo/wgcna/TraitsClean.txt
demo/wgcna/exprMat.txt
demo/wgcna/traitData.txt
man/DESeq2_ysx.Rd
man/Matrix2colCorrelation.Rd
man/WGCNA_GeneModuleTraitCoorelation.Rd
man/WGCNA_MEs_traitCorrelationHeatmap.Rd
man/WGCNA_ModuleGeneTraitHeatmap.Rd
man/WGCNA_coexprNetwork.Rd
man/WGCNA_cytoscape.Rd
man/WGCNA_cytoscape_each_module.Rd
man/WGCNA_dataCheck.Rd
man/WGCNA_dataFilter.Rd
man/WGCNA_filterTrait.Rd
man/WGCNA_hubgene.Rd
man/WGCNA_moduleTraitPlot.Rd
man/WGCNA_onestep.Rd
man/WGCNA_readindata.Rd
man/WGCNA_sampleClusterDetectOutlier.Rd
man/WGCNA_saveModuleAndMe.Rd
man/WGCNA_softpower.Rd
man/base_plot_save.Rd
man/checkAndInstallPackages.Rd
man/clusterSampleHeatmap2.Rd
man/clusterSamplePheatmap.Rd
man/clusterSampleUpperTriPlot.Rd
man/dataFilter.Rd
man/deseq2normalizedExpr.Rd
man/dh.Rd
man/draw_colnames_custom.Rd
man/enrichCustomizedPathway.Rd
man/enrichGO_model.Rd
man/enrichKEGG_model.Rd
man/find_coordinates.Rd
man/flower_plot.Rd
man/flower_plot_inner.Rd
man/generateAbundanceDF.Rd
man/generate_color_list.Rd
man/get_lower_tri.Rd
man/get_matched_columns_based_on_value.Rd
man/get_upper_tri.Rd
man/mixedToFloat.Rd
man/multipleGroupDEgenes.Rd
man/normalizedExpr2DistribBoxplot.Rd
man/numCheck.Rd
man/pca_run.Rd
man/rankPlot.Rd
man/readscount2deseq.Rd
man/salmon2deseq.Rd
man/sp.is.null.Rd
man/sp_EulerDiagrams.Rd
man/sp_barplot.Rd
man/sp_boxplot.Rd
man/sp_corrplot.Rd
man/sp_current_time.Rd
man/sp_dendextend.Rd
man/sp_determine_log_add.Rd
man/sp_enrichment.Rd
man/sp_get_ggplot_limits.Rd
man/sp_ggplot_add_vline_hline.Rd
man/sp_ggplot_facet.Rd
man/sp_ggplot_layout.Rd
man/sp_hclust.Rd
man/sp_histogram.Rd
man/sp_lines.Rd
man/sp_load_font.Rd
man/sp_manhattan2_plot.Rd
man/sp_manual_color_ggplot2.Rd
man/sp_manual_fill_ggplot2.Rd
man/sp_pca.Rd
man/sp_pcoa.Rd
man/sp_pheatmap.Rd
man/sp_raincloud.Rd
man/sp_readTable.Rd
man/sp_read_in_long_wide_matrix.Rd
man/sp_scatterplot.Rd
man/sp_set_factor_order.Rd
man/sp_string2vector.Rd
man/sp_transfer_one_column.Rd
man/sp_tree_plot.Rd
man/sp_upsetview.Rd
man/sp_vennDiagram.Rd
man/sp_vennDiagram2.Rd
man/sp_vennDiagram3.Rd
man/sp_volcano_plot.Rd
man/sp_writeTable.Rd
man/stackVlnPlot.Rd
man/stackVlnSeuratPlot.Rd
man/twoGroupDEgenes.Rd
man/value.identical.Rd
man/volcanoPlot.Rd
man/waterfalls_plot.Rd
man/widedataframe2boxplot.Rd
test/24_2_WGCNA_simple.Rmd
test/DESeq2_usage.Rmd
test/Plotusage.Rmd
test/WGCNA_usage.Rmd
test/test.Rmd
vignettes/.history
vignettes/Euler.txt
vignettes/Plot.Rmd
vignettes/Plot.sh
vignettes/Set.data
vignettes/bar.data
vignettes/bar.txt
vignettes/barplot_demo4.txt
vignettes/box.data
vignettes/boxplot_singlecell.txt
vignettes/ehbio.simplier.DESeq2.untrt._vs_.trt.results.xls
vignettes/enrichment.data
vignettes/exprMat.txt
vignettes/exprTable.annocol.txt
vignettes/exprTable.annorow.txt
vignettes/exprTable.txt
vignettes/exprTableWithReps.txt
vignettes/goeast.enrich.txt
vignettes/group_pcoa.data
vignettes/histogram.data
vignettes/histogram.demo1.txt
vignettes/inflectionpoint.txt
vignettes/iqtree.aligned.fa
vignettes/iqtree.treefile
vignettes/line.data
vignettes/manhattan.data
vignettes/metadata.txt
vignettes/pca.data
vignettes/pca_group.data
vignettes/pcoa.data
vignettes/scatter.txt
vignettes/scatter3.txt
vignettes/scatter_demo1.txt
vignettes/scatter_demo2.txt
vignettes/test.Rmd
vignettes/tree.attribute
vignettes/upset.txt
vignettes/upset.wide.data
vignettes/upsetview.data
vignettes/vennDiagram.data
vignettes/volcano.demo
vignettes/volcano.txt
vignettes/volcano2.txt
