Michael Kaufman's repositories
fastq-barcode-check
Rust code to check FASTQ reads for the presence of barcode sequences.
fuzzy-fastq
A bioinformatics script for matching DNA sequences with predefined barcodes and adapters using a mismatch threshold, then visualizing the distribution of matches in FASTQ files.
rna-seq-star-deseq2
bulk RNAseq workflow using Snakemake
10X_snakepipe
A snakemake pipeline for 10X genomics cellranger
addgene-stats
Plasmid request stats for my submissions to Addgene
brzezinski-lab-tools
Collection of quick tools for repetitive tasks in the Brzezinski Lab. Also serves as a demo for deploying a Python app from GitHub to Heroku.
combine_pdfs
Python script to combine multiple pdfs into a single pdf.
docker-scrnaseq-rstudio
Docker image for scRNA-seq analysis using RStudio.
gene_annotate
Tool to annotate csv or tsv files containing a column of gene symbols. Outputs formal gene name and protein function/class to table.
mlktools
Various tools to support day to day processing and workflows
py-enhancer-scanner
python implementation of an API to facilitate the scanning, integrating, and visualizing genomic track data for regions of interest in gene regulation
cookiecutter-data-snake
Reproducible data science template using Python, snakemake, mamba and more
cookiecutter-reproducible-research
A cookiecutter template for reproducible research projects using Python, Snakemake, and Pandoc.
cookiecutter-snakemake
A cookiecutter template for snakemake projects used in the Simpson Lab
docker-scrnaseq-jupyter
Docker image for scRNA-seq analysis using Jupyter Lab with kernels for both R and Python.
fast5check
A CLI tool to check for truncations in fast5 files.
htmltabs
A CLI tool to merge HTML files into a single HTML file with tabs.
pipeline-nanopore-ref-isoforms
Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools
pipeline-transcriptome-de
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
rstudio-m1
Dockerfile for RStudio Server on M1
snakemake-pipeline-template
Cookiecutter template for Snakemake pipelines
STARCH
Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
streamlit-nginx
streamlit-nginx is a Docker image with Streamlit and Nginx for web-based demo applications in Python 3.6 and above, in a single container.
TALON
Technology agnostic long read analysis pipeline for transcriptomes