R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
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Updated
Feb 15, 2024 - R
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
R package to work with ctDNA sequencing data
A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
A tutorial on structural variant calling for short read sequencing data
Add functional variant annotation to MAF file
Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape
💹 The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center …
Plot Protein: Visualization of Mutations
Plot Protein: Visualization of Mutations with Conservation
Matrix-like representations of mutation and CN data
Short Linear Motif (SLiM) Analysis in the context of human diseases
R Shiny based lightweight mutation exploration tool
R tools to mine & craft somatic mutations from cancer genomes
Useful scripts I've written during my dissertation research.
Identify synthetic lethal partners for tumour mutations.
This plot is useful for the comparison of mutational load across the cancer types, with input data in 2 coulmns i.e cancer types and mutatonal load for each samples in specificed cancer type.
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