Michael Weinstein's Projects
This program can take a tab-delimited text file containing bam file paths and loci and create a subdirectory of image captures for you.
Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency
Payloads for the Hak5 Bash Bunny
Designed to run on an SGE cluster, this program will take multiple BSMAP output datasets and quickly combine them into either a flat table OR a pickled file for analysis in Pandas (via python).
Repo for assisting on CRISPR project
Rosalind Problems for BIG 2022
Big Summer 2024 Example Code
Statistical demo for question that was asked
Python objects for finding reverse complements (and teaching object-oriented python)
Utility for adding some basic dbSNP annotation to a seattleseq output using only the dbSNP VCF. No major updates for the PERL version will be done, as it will be entirely rewritten in Python when the new VCF is released (expected in Nov 2014) and will be based off of the ExACto program.
Used for data other scripts need to pull down
Temporary repo for code handling DNA as binary. This will go away when integrated into a larger project.
This program is designed to look for potential off-target hits by any Cas9-Crispr type of system, including ones from alternate species with different PAM sites. This program requires python3 and a cluster system wtih a job queue such as openSGE or similar as well as an active connection to the Internet. The package dependencies were kept intentionally small, so that you should be able to copy this program to its own directory and be ready to run it out of the box.
Updated version, now gives structured indexed genomes for much faster searching.
dsNickFury is for comparing a CRISPR target site against all other potential sites in a genome. Orchid is a package I'm developing to go with it for iterative CRISPR analysis over an exome.
Easy multiprocessing tool for when multiprocessing should be easy. Demo for OCPython group April 2018.
End-to-end guide design for CRISPR/Cas9 with machine learning
Utility for using the ExAC VCF to annotate variants output from another variant effect predictor/annotation program
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
Long-awaited update for Figaro
Script for automating GATK scatter/gather job submissions based on directory structure of the BAM files
For sharing GATK plotting notebooks
Analysis pipeline for the GUIDE-seq assay. For news, see:
Simple script for determining if a hash (MD5) of a password has been broken.
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
Informatics challenge answer submission
Katacoda Scenarios
aMino Acid Reversing Application
Repo for public-facing 16s miq score