Name: Michael Kaufman
Type: User
Company: University of Colorado Anschutz Medical Campus
Bio: Informatics Fellow for the RNA Bioscience Initiative at the University of Colorado Anschutz Medical Campus
• PhD in Cell, Stem Cell, and Developmental Biology
Location: Aurora, Colorado
Michael Kaufman's Projects
A snakemake pipeline for 10X genomics cellranger
Series of python programs for the analysis of rodent behavior.
Plasmid request stats for my submissions to Addgene
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.
Python script to combine multiple pdfs into a single pdf.
Reproducible data science template using Python, snakemake, mamba and more
A cookiecutter template for reproducible research projects using Python, Snakemake, and Pandoc.
A cookiecutter template for snakemake projects used in the Simpson Lab
Docker image for scRNA-seq analysis using Jupyter Lab with kernels for both R and Python.
Docker image for scRNA-seq analysis using RStudio.
Rename image files based upon stored EXIF data.
A CLI tool to check for truncations in fast5 files.
Rust code to check FASTQ reads for the presence of barcode sequences.
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.
Tool to annotate csv or tsv files containing a column of gene symbols. Outputs formal gene name and protein function/class to table.
A CLI tool to merge HTML files into a single HTML file with tabs.
Various tools to support day to day processing and workflows
Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
python implementation of an API to facilitate the scanning, integrating, and visualizing genomic track data for regions of interest in gene regulation
A Snakemake pipeline for cellranger to process 10x single-cell RNAseq data
bulk RNAseq workflow using Snakemake
Dockerfile for RStudio Server on M1