sbamin

canineglioma

Comparative molecular life history of spontaneous canine and human gliomas. Amin et al. Cancer Cell 2020

code101

My notes on programming, mostly using R, Python, and bash.

canine_gistic2

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

gwa_tutorial

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.

theme-mkdocs-material

Forked from https://github.com/squidfunk/mkdocs-material

sitebuilder

Dockerfile to build jekyll/hugo/mkdocs-based website

BISCUT-py3

Code from Shih J, Sarmashghi S et al. 2023: https://pubmed.ncbi.nlm.nih.gov/37380777/

CellProfileR

R scripts to clean/analyse CellProfiler output, forked from

cytominerDev

Forked from https://github.com/cytomining/cytominer

flowr

Robust and efficient workflows using a simple language agnostic approach

image_analysis_training

repo for training materials - forked from https://github.com/erickmartins/training

imgsc_issue_cp_metadata

code towards an issue posted on image.sc forum

introductory-statistics-with-r

ISLR-tidymodels-labs

Credir: Sourced from https://github.com/EmilHvitfeldt/ISLR-tidymodels-labs ; Issues at the author's site, https://github.com/EmilHvitfeldt/ISLR-tidymodels-labs/issues

kitty-config

My current Kitty configuration

machine-learning-for-biomedical-science

ML-from-zavalab

forked repo from zavalab/ML

python_for_microscopists_by_digitalsreeni

Author's youtube: https://www.youtube.com/@DigitalSreeni

re2

RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library.

sbamin

About

scopit

power analysis for single-cell experiments. Forked from https://github.com/navinlabcode/scopit by Davis A, Gao R, Navin NE. SCOPIT: sample size calculations for single-cell sequencing experiments. BMC Bioinformatics 2019;20:566. https://doi.org/10.1186/s12859-019-3167-9.

ShatterSeek

Forked from https://github.com/parklab/ShatterSeek

shell-novice

The Unix Shell, source forked from https://swcarpentry.github.io/shell-novice/

slurmR

slurmR: A Lightweight Wrapper for Slurm

smk-simple-slurm

Forked from https://github.com/jdblischak/smk-simple-slurm

snakemake-tutorial-data

Example data for the official Snakemake tutorial

snakemake-wrappers

Forked from the upstream source: https://github.com/snakemake/snakemake-wrappers

toymake_hpc

Snakemake workflow for JAX HPC Sumner

vcf2maf

Forked version from

ycrc.github.io

documentation repo for the YCRC, see src branch for more info