Page Index - labbces/sugarcane_RNAome GitHub Wiki
26 page(s) in this GitHub Wiki:
- Home
- Multi-genotype analyses of long-ncRNAs in Sugarcane
- Identification of long non-coding RNAs in sugarcane
- Conserved long non-coding RNAs in the panRNAome
- Families/classes of lncrnas
- Co-expression patterns of lncRNAs
- Aggregating the consensus of putative ncRNAs predicted by the 3 tools
- Analyzing MCL clusterings (effects of Inflation value)
- Analyzing Network Metrics
- Analyzing RNA expression patterns after filtering
- Annotation of ncRNAs families
- Calculating the RNA expression for each sample
- Clustering co‐expressed modules
- Clustering sequences by identity
- Computing gene pair relationships with Pearson correlation
- Contrasting genotypes selection
- Filtering the RNAs expression matrix by function
- Filtering the RNAs expression matrix of the contrasting genotypes
- Finding conserved modules of co‐expression (complete subgraphs ‐ cliques)
- Gene Ontology enrichment analysis: exploring biological function of modules
- Inference of the pan‐ncRNAome
- Predicting putative lncRNAs with CPC2
- Predicting putative lncRNAs with PLncPRO
- Predicting putative lncRNAs with RNAplonc
- Principal Component Analysis of lncRNAs expression in contrasting genotypes
- Visualizing co‐expressed gene modules in contrasting genotypes