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10x_snakepipe

A snakemake pipeline for 10X genomics cellranger

activitytesting-suite

Series of python programs for the analysis of rodent behavior.

addgene-stats

Plasmid request stats for my submissions to Addgene

bioinformaticslife-blog

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.

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-images

docker-scrnaseq-jupyter

Docker image for scRNA-seq analysis using Jupyter Lab with kernels for both R and Python.

docker-scrnaseq-rstudio

Docker image for scRNA-seq analysis using RStudio.

drop-bashjob

exif_renamer

Rename image files based upon stored EXIF data.

fast5check

A CLI tool to check for truncations in fast5 files.

fastq-barcode-check

Rust code to check FASTQ reads for the presence of barcode sequences.

fastq-rs

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.

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.

geneplot

htmltabs

A CLI tool to merge HTML files into a single HTML file with tabs.

mlkaufman.github.io

mlktools

Various tools to support day to day processing and workflows

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

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

pyflow-cellranger

A Snakemake pipeline for cellranger to process 10x single-cell RNAseq data

python-sourced

rna-seq-star-deseq2

bulk RNAseq workflow using Snakemake

rstudio-m1

Dockerfile for RStudio Server on M1