- Vst and normalized count data generated using the DESeq2
- TPMs generate with a second pipeline using CLC Workbench
- WGCNA to generate conserved Module assignments and Hub-genes
- Python scripts
- Script for Supercluster detection
- miRNA Edge Database construction
- Hub-gene networks and miRNA:hub-gene target-spaces
- miRNA enrichment analysis and mRNA disease affiliation analysis
- Gene enrichment and disease analysis
- NOCICEPTRA Tool at Docker
RNA and small RNA sequencing were aligned to the human reference genome GRCH.38.p13 (genecode) with the spice-aware STAR-aligner and the parameter as indicated in the Publication and normalized using DESseq2. TPMs were generated with a second pipeline using CLC-workbench with the GRCh38.p7 reference genome from the NCBI webpage
For both small and long RNA sequencing only unqiuely matched reads were counted.Multimappers for miRNAs and ncRNAs were added in the files multimapper section and in the NOCICEPTRA Tool