Man pages for Facottons/DOAGDC
A Package to Download, Organize and Analyze Genomic Data Commons (GDC) Data
| annotation_table | UCSC refseq table |
| beta2m_values | Convert beta values to mvalues |
| clinical_terms | Search for clinical terms for all available tumors |
| co_expression | Co-Expression Analyses |
| concatenate_exon | Concatenate GDC files into a single matrix and prepar the... |
| concatenate_expression | Concatenate GDC files into a single matrix and prepar the... |
| concatenate_methylation | Concatenate GDC files into a single matrix and prepar the... |
| concatenate_mirna | Concatenate GDC files into a single matrix and prepar the... |
| concatenate_mutation | Concatenate GDC files into a single matrix and prepar the... |
| concatenate_protein | Concatenate GDC files into a single matrix and prepar the... |
| cross_co_expression | Cross co-expression gene list against differential expression... |
| dea_deseq2 | Run DESeq2 gene Differential Expression Analysis (DEA). |
| dea_ebseq | Run EBSeq gene Differential Expression Analysis (DEA). |
| dea_edger | Run edgeR gene Differential Expression Analysis (DEA). |
| do_react_enrich | DESEASE-ONTOLOGY and REACTOME ENRICHMENT |
| download_gdc | Download data from GDC Data Portal and GDC Legacy Archive |
| draw_heatmap | Draw a heatmap |
| gonto | Perform Gene-Ontology Pathways Enrichment |
| groups_identification_cox_hr | Separate patients in groups |
| groups_identification_mclust | Separate patients in groups |
| gsea | Gene Set Enrichment Analysis |
| pca_analysis | Generate plot for Principal Component Analysis |
| table2_doagdc | From global to DOAGDC environment |
| venn_diagram | Venn diagram of differential expression genes list |
