Page Index - labbces/sugarcane_RNAome GitHub Wiki

49 page(s) in this GitHub Wiki:

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