michael-weinstein Goto Github PK

autoigv

This program can take a tab-delimited text file containing bam file paths and loci and create a subdirectory of image captures for you.

azimuth

Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency

bashbunny-payloads

Payloads for the Hak5 Bash Bunny

battlestar

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).

biggmaestro

Repo for assisting on CRISPR project

bigsummer2022

Rosalind Problems for BIG 2022

bigsummer2024pythonworkshop2

Big Summer 2024 Example Code

bootstrapwithoutlier

Statistical demo for question that was asked

color_chart

complement

Python objects for finding reverse complements (and teaching object-oriented python)

dbsnperator

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.

dls

Used for data other scripts need to pull down

dnabinarytemp

Temporary repo for code handling DNA as binary. This will go away when integrated into a larger project.

dsnickfury

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.

dsnickfury2

Updated version, now gives structured indexed genomes for much faster searching.

dsnickfury3plusorchid

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.

easymultiprocessing

Easy multiprocessing tool for when multiprocessing should be easy. Demo for OCPython group April 2018.

elevation

End-to-end guide design for CRISPR/Cas9 with machine learning

exacto

Utility for using the ExAC VCF to annotate variants output from another variant effect predictor/annotation program

figaro

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters

figaro2

Long-awaited update for Figaro

gatkbydirectory

Script for automating GATK scatter/gather job submissions based on directory structure of the BAM files

gatkplot

For sharing GATK plotting notebooks

guideseq

Analysis pipeline for the GUIDE-seq assay. For news, see:

hash-sambrada

Simple script for determining if a hash (MD5) of a password has been broken.

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

informaticschallenge092019

Informatics challenge answer submission

katacoda-scenarios

Katacoda Scenarios

mara

aMino Acid Reversing Application

miqscore16spublic

Repo for public-facing 16s miq score