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riboPLATE-seq: code required for analysis and interpretation of riboPLATE-seq data Organization of repository: scripts/ -- contains main Jupyter notebook (riboPLATEseq.ipynb) and the scripts it calls data/ -- contains input count matrices and barcode files workingdir/ -- temporary directory for intermediate output, e.g. DESeq2 results and normalized counts gsea/ -- temporary directory for GSEA output specifically ReferenceInfo/ -- contains gene lists of interest, should hold GTF file as well (GTF too large to distribute on Github) outdir/ -- Final output files, i.e. figures Notebook requres GRCh38 RefSeq GTF annotations, available from https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39 Notebook also requires GSEA command-line installation -- set 'gspath' variable in the notebook to the directory containing GSEA
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Notebook and associated scripts for interpretation of riboPLATE-seq data
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