Name: Shaghayegh Soudi (PhD, MSc)
Type: User
Company: Stanford Radiation Oncology
Bio: Research Scientist-Computational Oncology.
I am interested in understanding genetic/non-genetic
mechanisms of cancer evolution and therapy resistance
Twitter: ShaghayeghSoudi
Location: Stanford
Shaghayegh Soudi (PhD, MSc)'s Projects
ATAC-Seq, ChIP-Seq, and whole genome bisulfite! An introduction to analyzing some of the most popular types of epigenetic data.
Battenberg R package for subclonal copynumber estimation
customized version of Battenberg which includes min and max rho desired ranges and subsequent R script modifications
Supplementary files for my book, "Bioinformatics Data Skills"
Bioinformatics with Python Cookbook, Third Edition
Course material for UBC Biol525D
Detecting DNA methylation from PacBio CCS reads
dN/dS methods to quantify selection in cancer and somatic evolution
Dirichlet Process based methods for subclonal reconstruction of tumours
Dirichlet Process Clustering Pre-Processing Pipeline
Sarcoma epigenomics projects
Code accompanying The Evolutionary history of 2,658 cancers
fastqcr: Quality Control of Sequencing Data
Scripts for running GWAS analysis and visualizing the results
all scripts for GWAS and convergence analysis in wild sunflowers
Collection of standard analytical pipelines for genomic and transcriptomic data
This repository contain pipelines and scripts for analyzing long-read sequencing data
A suite of tools for Archetype Analysis, plasticity calculations, and visualization applied to SCLC single cell data.
R function for calculating the timing of DNA aberration events from NGS data.
An R package to time somatic mutations
Open MPI main development repository
Code for mutational timing of gains and signatures analysis