Eitan and Amrom Data Science in Molecular Pathology Repository

Open-Source Tools for NGS Data Analysis and Visualization

Overview

This repository contains Jupyter notebooks focused on molecular pathology analysis, visualization, and interpretation.

Notebook	Description	Colab
Chekc Contamination	Using a 'Master File' of Variants On Multiple Specimens, Determine If Any Specimens Seem Contaminated
MAF2BAF	Convert an MAF to a BAF for visualizing b-allele frequency in IGV
Variant Table to Bed File	Process a table of variants to a bed formatted file
A Streamlit GUI to Visualize B-allele frequency	Make a streamlit app and run from colab
Gnomad Match and plot	Plot gnomad frequencies to check concordnace with known information
Variant File Annotated	Annotate and visualize variant files

Name		Name	Last commit message	Last commit date
Latest commit History 33 Commits
Education		Education
README.md		README.md
find_matching_snp_betweensamples_onarun.ipynb		find_matching_snp_betweensamples_onarun.ipynb
makebaf_bedgraphfile.ipynb		makebaf_bedgraphfile.ipynb
makingbedfilefromlargetableofvariants.ipynb		makingbedfilefromlargetableofvariants.ipynb
pathologist_datascientist.jpeg		pathologist_datascientist.jpeg
plot_baf.ipynb		plot_baf.ipynb
seebaf_values_over_segments.ipynb		seebaf_values_over_segments.ipynb
test_ethnicity_using_gnomad_af.ipynb		test_ethnicity_using_gnomad_af.ipynb
variantfile_annotated.ipynb		variantfile_annotated.ipynb