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SLAM-seq PAIP1 Analysis Pipeline v1.0.1

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@ivanek ivanek released this 19 Aug 11:45
· 3 commits to main since this release
v1.0.1
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SLAM-seq PAIP1 Analysis Pipeline v1.0.1

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.

Notes

prepare_MSigDb.R script was moved to separate repository https://github.com/dbmbcf/msigdb_preprocessing

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