Samir Amin's Projects
Advanced R: a book
Code from Shih J, Sarmashghi S et al. 2023: https://pubmed.ncbi.nlm.nih.gov/37380777/
Source: cancerTiming by Purdom et al. 2013
Canine CanFam3.1 GISTIC2 copy number analysis. For debugging GISTIC2 .mat file, please contact developers at https://www.genepattern.org/modules/docs/GISTIC_2.0) or https://groups.google.com/a/broadinstitute.org/g/gistic-forum
Comparative molecular life history of spontaneous canine and human gliomas. Amin et al. Cancer Cell 2020
R scripts to clean/analyse CellProfiler output, forked from
(Beta) Germline workflow for Canine Glioma Project - Stage for Nextflow
Batch upload bam files to NCBI SRA using aspera
My notes on programming, mostly using R, Python, and bash.
Forked from https://github.com/cytomining/cytominer
This Snakemake pipeline implements the GATK best-practices workflow
Dockerfile for DNA Nexus NGS tools
dN/dS methods to quantify selection in cancer and somatic evolution; forked for canine genome. Original code is by @im3sanger at
Theme for documentation, forked from
Robust and efficient workflows using a simple language agnostic approach
docker container for running NCI GDC gdc-client
git landing page
Forked from https://github.com/MareesAT/GWA_tutorial. Cite: 1 Marees AT, de Kluiver H, Stringer S, Vorspan F, Curis E, Marie-Claire C, et al. A tutorial on conducting genome-wide association studies: Quality control and statistical analysis. Int J Methods Psychiatr Res 2018;27:e1608. https://doi.org/10.1002/mpr.1608.
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
repo for training materials - forked from https://github.com/erickmartins/training
code towards an issue posted on image.sc forum
Credir: Sourced from https://github.com/EmilHvitfeldt/ISLR-tidymodels-labs ; Issues at the author's site, https://github.com/EmilHvitfeldt/ISLR-tidymodels-labs/issues
Comments over github issue for jekyll blog
My current Kitty configuration
forked repo from zavalab/ML
Author's youtube: https://www.youtube.com/@DigitalSreeni
:notebook: Data Carpentry R lessons on ecology.