deepsubs
Deepak Subramanian
Recently Published
Tumour sequencing data filtering R script for ‘Assessment of candidate high-grade serous ovarian carcinoma predisposition genes through integrated germline and tumour sequencing’ (Subramanian et al., npj Genomic Medicine, 2024)
R code used for tumour exome and genome sequencing data analysis, as described in the Methods section of the above paper.
Thesis SIGNAL Mutational Signature GLMM Testing Script
Script for testing of generalised linear mixed-effect modelling (GLMM) used for tumour exome SIGNAL mutational signature statistical comparisons, as described in Chapter 4.2.2.4.
Thesis SIGNAL Mutational Signatures GLMM Comparison Script
Script for tumour exome SIGNAL mutational signature statistical comparisons using generalised linear mixed-effect modelling (GLMM), as described in Chapter 4.2.2.4. A modified version of this script was used for batch processing of multiple individual sample files (available from the author on reasonable request).
Thesis Tumour Exome Mutational Signature Analysis Script
Script used for tumour exome mutational signature analysis (for the somatic variant file only), using SignatureEstimation with the COSMIC v2 and v3 signature sets, as described in Chapter 4.2.2.2. A modified version of this script was used for batch processing of multiple files (available from the author on reasonable request).
Thesis Tumour Exome Variants Filtering Script
Script used for tumour exome variant filtering (for both somatic and tumour-only variant files), as described in Chapter 4.1.2.2. A modified version of this script was used for batch processing of multiple files (available from the author on reasonable request).
Thesis Missense Variants LoF-Enriched Genes Random Sampling Script
Script used for variant random sampling analysis, as described in Chapter 3.2.2.3.
Thesis Missense Variant GnomAD-Depleted Genes Script
Script used for variant analysis, as described in Chapter 3.2.2.4.
Thesis Missense Variant LoF-Enriched Genes Script
Script used for variant analysis, as described in Chapter 3.2.2.3.
Thesis Missense Variant AF Analysis Script
Script used for variant analysis, as described in Chapter 3.2.2.2.
Thesis Low-Frequency DNA Repair Genes Somatic LoF Variants Filtering Script
Script used for low-frequency LoF variant filtering and analysis, as described in Chapter 3.3.2.1.
Thesis MGRB Data Comparison Script
Script used for MGRB comparison of candidate genes, as described in Chapter 3.1.2.3.
Thesis LoF Variant Burden Analysis Script
Script used for variant analysis, as described in Chapter 3.1.2.1.
Thesis Synonymous Variants Analysis Script
Script used for variant analysis, as described in Chapter 3.1.2.2.
Thesis LoF Variants Filtering and Analysis by Age Script
Script used for variant analysis, as described in Chapter 3.1.2.1.
Thesis LoF Variants Filtering and Analysis by Family History Script
Script used for variant analysis, as described in Chapter 3.1.2.1.
Thesis Non-Protein-Coding Variants Filtering and Analysis Script
Script used for variant analysis, as described in Chapter 3.1.2.1.
Filtering and ranking R script for ‘Exome sequencing of familial high-grade serous ovarian carcinoma reveals heterogeneity for rare candidate susceptibility genes’ (Subramanian et al., Nature Communications, 2020)
R code used for exome sequencing data analysis, as described in the Methods section of the above paper.