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SLAM-seq PAIP1 Analysis Pipeline v1.0.0

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@ivanek ivanek released this 19 Aug 06:58
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v1.0.0
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SLAM-seq PAIP1 Analysis Pipeline v1.0.0

Analysis scripts for SLAM-seq–based mRNA stability profiling of PAIP1 wild-type (WT), overexpression (OE), and knockdown (KD) genotypes.

Included scripts

  • analysis_mRNASeq.qmd : differential expression analysis (edgeR QL-GLM) and GSEA (CAMERA) across genotypes and timepoints.
  • analysis_halflifes.qmd : mRNA half-life estimation from T-to-C conversion rates using three complementary approaches (NLS, limma, edgeR), with cross-model comparison and genotype-level statistics.
  • prepare_MSigDb.R : preprocesses a local MSigDB SQLite dump into per-gene-set symbol/Entrez/Ensembl mappings and C1 positional GRanges, ready for use in the GSEA step above.

Notes

Requires data from GEO GSE339524 and MSigDB gene sets downloaded separately (see README).

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