Modules

• Introduction
• Quality Submodules
  • pyseqrna.quality_check module
    • fastqcRun()
  • pyseqrna.quality_trimming module
    • flexbarRun()
    • trim_galoreRun()
    • trimmomaticRun()
  • pyseqrna.ribosomal module
    • sortmernaRun()
• Alignment Submodules
  • pyseqrna.aligners module
    • STAR_Aligner
      • STAR_Aligner.build_index()
      • STAR_Aligner.check_index()
      • STAR_Aligner.run_Alignment()
    • hisat2_Aligner
      • hisat2_Aligner.build_index()
      • hisat2_Aligner.check_index()
      • hisat2_Aligner.run_Alignment()
  • pyseqrna.pyseqrna_stats module
    • align_stats()
• Quantification Submodules
  • pyseqrna.quantification module
    • featureCount()
    • htseqCount()
  • pyseqrna.multimapped_groups module
    • countMMG()
  • pyseqrna.normalize_counts module
    • Normalization
      • Normalization.CPM()
      • Normalization.RPKM()
      • Normalization.TPM()
      • Normalization.meanRatioCount()
    • boxplot()
  • pyseqrna.clustering module
    • clusterSample()
    • leaf_label()
• Differential Genes Submodules
  • pyseqrna.differential_expression module
    • Gene_Description
      • Gene_Description.add_names()
      • Gene_Description.add_names_annotation()
    • degFilter()
    • runDESeq2()
    • run_edgeR()
• Functional Annotation Submodules
  • pyseqrna.gene_ontology module
    • GeneOntology
      • GeneOntology.barplotGO()
      • GeneOntology.dotplotGO()
      • GeneOntology.enrichGO()
  • pyseqrna.pathway module
    • Pathway
      • Pathway.barplotKEGG()
      • Pathway.dotplotKEGG()
      • Pathway.enrichKEGG()
• Utility Submodules
  • pyseqrna.arg_parser module
  • pyseqrna.pyseqrna_utils module
    • PyseqrnaLogger()
    • add_MMG()
    • change_attribute()
    • change_ids()
    • check_files()
    • check_path()
    • check_status()
    • clusterRun()
    • findFiles()
    • getFiles()
    • getGenes()
    • get_basename()
    • get_cpu()
    • get_directory()
    • get_file_extension()
    • get_parent()
    • make_directory()
    • parse_config_file()
    • parse_gff()
    • read_input_file()
    • replace_cpu()
  • pyseqrna.version module
  • pyseqrna.pyseqrna_plots module
    • plotHeatmap()
    • plotMA()
    • plotVenn()
    • plotVolcano()