SERPINA3 is a marker of cartilage differentiation and drives extracellular matrix production in chondrogenesis

Comparative analysis of SERPINA3 knock-down in Chondrogenesis and Osteogenesis RNA-Seq time course data.

Running the analysis

With Singularity

Requires singularity to be installed

#download the data and code
git clone https://github.com/CBFLivUni/SERPINA3Chondrogenesis.git

#move the downloaded repositry 
cd d.wilk_serpins

#run the analysis using the singularity container with all the needed dependencies
singularity run https://pgb.liv.ac.uk/~jsoul/DW/runAnalysis.img

Manual installation and execution

#or install the needed R libraries
Rscript ./install/installRLibs.R

#run the analysis
Rscript runAnalysis.R

Directories & Files

• [DW_E36_120123_Osteogenesis,DW_E36_120123_Chondrogenesis].[DATE].R_session_info.txt contains the R session info for the run of the pipeline on that date.

• DW_E36_120123_Osteogenesis and DW_E36_120123_Chondrogenesis contains:

  • data contains expr, annot and metadata:

    • annot contains ID conversions from biomart and REACTOME pathway-wise gene sets.
    • expr contains .rds and .tsv counts/expression matrices from the SkeletalViz pipeline (https://github.com/soulj/SkeletalVis-Pipeline).
    • metadata contains metadata for the Osteogenesis and Chondrogenesis experiments, respectively. These are important for the running the .Rmd documents.

  • results contains deseq2, geva, qc and pathway:

    • deseq2 contains the results tables .tsv's for DESeq2.
    • geva contains the results tables .tsv's for GEVA (https://github.com/sbcblab/geva).
    • qc contains the quality control analyses, including the PCA score plots.
    • pathway contains the GSEA pathway analysis results.

• Rmds contains the R markdown (.Rmd) file used to analyses the gene expression data (post-Nextflow pipeline).

• extra_scripts contains helper functions in R scripts for the .Rmd document(s).

• install provides the installation script for the needed R libraries