SLAM-seq PAIP1 Analysis Pipeline v1.0.2

• Updated the text, added the prompt used to generate literature summary and draft of the methods.

SLAM-seq PAIP1 Analysis Pipeline v1.0.1

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

SLAM-seq PAIP1 Analysis Pipeline v1.0.0

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).