Man pages for ajitjohnson/arseq
Automated RNA Sequencing Analysis Pipeline
| arseq | Automated RNASeq Analysis Pipeline |
| arseq.deg.plot | Heatmap of the differentially expressed genes |
| arseq.ensembl2genename | Gene ID converter |
| arseq.euclid.dist | Euclidean distance |
| arseq.euclid.dist.plot | Euclidean distance heatmap |
| arseq.go.enrich | Gene Ontology (GO) term enrichment |
| arseq.go.enrich.plot | Gene Ontology (GO) term enrichment |
| arseq.gsea | Gene Set Enrichment Analysis (GSEA) |
| arseq.gsea.preprocess | GSEA pre-processing step |
| arseq.gsea.runall | Bulk Gene Set Enrichment Analysis (GSEA) |
| arseq.kegg.enrich | KEGG pathway enrichment |
| arseq.kegg.enrich.plot | Gene Ontology (GO) term enrichment |
| arseq.kmeans | K Means clustering |
| arseq.kmeans.plot | K Means clustering Heatmap |
| arseq.kmeans.reactome.plot | Reactome Pathway Enrichment of Kmeans clustering output |
| arseq.mds.plot | Multidimensional scaling (MDS) Analysis |
| arseq.mvg | Most Variable Genes |
| arseq.mvg.plot | Most Variable Genes |
| arseq.pca | Principal Component Analysis |
| arseq.pca.plot | Principal Component Analysis |
| arseq.pheatmap | Pheatmap plotting function |
| arseq.plot.save | Save plots |
| arseq.poisd.dist | Poisson distance |
| arseq.poisd.dist.plot | Poisson distance heatmap |
| arseq.reactome.enrich | Reactome enrichment Analysis |
| arseq.volcano.plot | Volcano Plot |
| bods | bods |
| dot-onAttach | Startup Message |
| example_data | Counts table |
| example_dds | DESeq2 object |
| example_deg | Differentially expressed genes |
| example_meta | Meta data |
| g_variables | Global variables |
| kegg.sets.hs | kegg.sets.hs |
| my_plots | my_plots |
