NGN3_paper_code

Source codes to perform computational analyses in NGN3 paper

Methods and Tools

• RNA-seq transcript quantification: RSEM
• RNA-seq read alignment: STAR
• Differential gene expression (DGE): DESeq2
• Differential transcript expression (DTE): DESeq2
• Gene ontology enrichment: PANTHER
• Differential transcript usage (DTU): IsoformSwitchAnalyzeR
• Differential splicing events: rMATS
• RBP consensus motif enrichment: rMAPS2
• CLIP-seq binding site enrichment: RBP-Maps
• ONT-seq transcript identification and quantification: IsoTV
• ONT-seq transcript classification: SQANTI3
• Protein identification and quantification: MaxQuant
• Differential protein enrichment: DEP

Directory structure

.
├── ONT_seq_analysis                                      # Scripts used for ONT-seq analyses
│   ├── DTE_analysis                                      # Differential transcript expression (DTE) analysis
│   ├── DTU_analysis                                      # Differential transcript usage (DTU) analysis
│   ├── long_short_comparison                             # Comparison between ONT-seq and Illumina RNA-seq
│   ├── quantification_classification                     # transcript identification, quantification and classification for ONT-seq data
├── Proteomics_analysis                                   # Scripts used for Proteomics analyses
│   ├── IsoformMS                                         # Protein isoform quantification for mass spectrometry (MS)
│   ├── PrepareData                                       # Pre-processing
│   ├── RBPs                                              # Differential analysis for RNA binding proteins (RBPs)
├── RNA_seq_analysis                                      # Scripts used for RNA-seq analyses
│   ├── DGE_analysis                                      # Differential gene expression (DGE) analysis
│   ├── DTU_analysis                                      # Differential transcript usage (DTU) analysis
│   ├── GO_enrichment_analysis                            # Gene ontology enrichment analysis
│   ├── RBP_binding_site_analysis                         # RBP binding sites enrichment
│   ├── RBP_consensus_motif_analysis                      # RBP consensus motifs enrichment
│   ├── comparative_transcriptome_analysis_with_BrainSpan # Comparison of transcriptomes between BrainSpan and NGN3 models
│   ├── differential_splicing_analysis                    # Event-centered differential splicing analysis
│   ├── quantification                                    # transcript quantification for RNA-seq data
└── ...