Pinned Repositories
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
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.
gdc-client
docker container for running NCI GDC gdc-client
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.
sitebuilder
Dockerfile to build jekyll/hugo/mkdocs-based website
sbamin's Repositories
sbamin/canineglioma
Comparative molecular life history of spontaneous canine and human gliomas. Amin et al. Cancer Cell 2020
sbamin/code101
My notes on programming, mostly using R, Python, and bash.
sbamin/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
sbamin/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.
sbamin/theme-mkdocs-material
Forked from https://github.com/squidfunk/mkdocs-material
sbamin/sitebuilder
Dockerfile to build jekyll/hugo/mkdocs-based website
sbamin/BISCUT-py3
Code from Shih J, Sarmashghi S et al. 2023: https://pubmed.ncbi.nlm.nih.gov/37380777/
sbamin/CellProfileR
R scripts to clean/analyse CellProfiler output, forked from
sbamin/cytominerDev
Forked from https://github.com/cytomining/cytominer
sbamin/flowr
Robust and efficient workflows using a simple language agnostic approach
sbamin/image_analysis_training
repo for training materials - forked from https://github.com/erickmartins/training
sbamin/imgsc_issue_cp_metadata
code towards an issue posted on image.sc forum
sbamin/introductory-statistics-with-r
sbamin/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
sbamin/kitty-config
My current Kitty configuration
sbamin/machine-learning-for-biomedical-science
sbamin/ML-from-zavalab
forked repo from zavalab/ML
sbamin/python_for_microscopists_by_digitalsreeni
Author's youtube: https://www.youtube.com/@DigitalSreeni
sbamin/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/sbamin
About
sbamin/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.
sbamin/ShatterSeek
Forked from https://github.com/parklab/ShatterSeek
sbamin/shell-novice
The Unix Shell, source forked from https://swcarpentry.github.io/shell-novice/
sbamin/slurmR
slurmR: A Lightweight Wrapper for Slurm
sbamin/smk-simple-slurm
Forked from https://github.com/jdblischak/smk-simple-slurm
sbamin/snakemake-tutorial-data
Example data for the official Snakemake tutorial
sbamin/snakemake-wrappers
Forked from the upstream source: https://github.com/snakemake/snakemake-wrappers
sbamin/toymake_hpc
Snakemake workflow for JAX HPC Sumner
sbamin/vcf2maf
Forked version from
sbamin/ycrc.github.io
documentation repo for the YCRC, see src branch for more info