README.md

# 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
    └── ...