Exercise - nibb-gitc/gitc2021mar-rnaseq GitHub Wiki

演習問題

NGSの基礎 1, 2

  • ex101 -- NGS基礎復習問題集 [Nishide]
  • ex201 -- IGVによる可視化 [Yamaguchi]

RNA-seq基礎 3

  • ex301 -- data import and visualization [shige]
  • ex302 -- MA plot [shige]
  • ex303 -- Volcano plot [shige]

RNA-seq解析パイプライン transcript-based (4) and genome-based (5) pipeline

  • ex401 -- Transcript-based RNA-seq pipeline: mapping-free pipeline using Salmon [shige]
  • ex402 -- edgeR: Differential expression analysis (classic) [shige]
  • ex403 -- [advanced] edgeR (linear model) [shige]
  • ex501 -- Genome-based RNA-seq pipeline (mapping and counting) [Yamaguchi]

多変量解析

  • ex601 -- 階層クラスタリング[Sato]
  • ex602 -- MDSによる可視化
  • ex603 -- k-means法による次元圧縮

RNA-seq解析パイプライン de novo 7

  • ex701 -- Trinity de novo assembly [shige]
  • ex702 -- BUSCO 練習 [shige]
  • ex703 -- BUSCO によるtranscritomeの評価 [shige]

アノテーションやGene Ontology解析

  • ex801 -- Annotation using similarity based methods [uchiyama]
  • ex802 -- GO enrichment analysis (with public annotation) [uchiyama]
  • ex803 -- GO enrichment analysis (with user annotation) [uchiyama]

実戦演習

  • case1 -- transcript-based RNA-seq, pair-wise comparison. (salmon/edgeR ) [shige]
  • case2 -- genome-based RNA-seq analysis (HISAT2/StringTie/edgeR workflow) [Yamaguchi]
  • case3 -- transcript-based RNA-seq, multivariate analysis of three samples including clustering (salmon/edgeR ) [shige]
  • case4 -- Annotate Trinity assembly using BLAST [shige]
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