Man pages for jmzeng1314/humanid
gene id annotation
| add_kegg_up_down_link | add links for the KEGG enrichment table. |
| batch_enrichment | enrichment for GO/KEGG |
| batch_pheatmap | Do batch heatmap for interested gene sets. |
| batch_t_test | do batch t.test for a matrix |
| cc_plot | plot overall/within group mean correlation coefficient of... |
| create_dup_exprSet | create the duplicated expression matrix |
| create_example_exprSet | create expression matrix,rowname are unique genes, colname... |
| create_genesets_list | create a list of gene sets for enzyme/protein complex/... |
| createGSEAinput | create gct file and cls files |
| do_DEG_2groups | Do differential expression analysis for the expression matrix |
| downGSE | download the data from GEO database |
| draw_boxplot_gene | draw boxplot for a specific gene's values between two groups |
| format_DEG | write some files from the DEG results from topTable(limma) |
| geneAnno | annotate gene name or map for entrez id or symbol |
| get_GSE_links | Get the links for GSE studyID |
| get_symbol_exprSet | extract the expression matrix from a eSet object |
| GSEA | Main GSEA Analysis Function that implements the entire... |
| hello | Hello, World! |
| hyperGtest_jimmy | Hypergeometric Tests for GO/KEGG test by jimmy |
| keggAnno | annotate KEGG pathway for entrez id or symbol |
| pathway_heatmap | draw heatmap for a single pathway or a batch of pahways |
| plot_ES_score | re-draw ES-score figures for GSEA |
| probesetAnno | annotate entrez gene id for the given probeset |
| pub_trend | visualization for the trend of reseach area based on some... |
| QCexpressionMatrix | Do basic QC for a expression matrix. |
| refreshMicroarrayData | extract probeset ID and entrez gene id from R packages |
| refreshOrgHsData | extract gene IDs from org.Hs.eg.db |
| rmDupID | remove duplicat gene entrez ID or symbol for a expression... |
| update_kegg | update kegg data |
| Volcanic_DEG | write some files from the DEG results from topTable(limma) |
