michael-weinstein
Bioinformatics and information security. B.Sc. in Microbiology, Immunology, and Molecular Genetics Ph.D. in Human Genetics Bench and bioinformatics
@tecangenomics Orange County, California
Pinned Repositories
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.
bashbunny-payloads
Payloads for the Hak5 Bash Bunny
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.
figaro
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
figaro2
Long-awaited update for Figaro
Prepared-SQL
Repository of prepared SQL queries for exome analysis. These assume that the tables were prepared using the scripts from my git (otherwise column names may vary). To use them, run a find/replace on the term in curly brackets (be sure that the seattleSeq table and corresponding VCF were named identically except for the VCF at the end).
W32-git-docker-example
Example repo for UCLA Collaboratory Workshop 32 on Github and Docker
w32-rps-Spring2024
Repo for the Spring 2024 Git and Docker class
michael-weinstein's Repositories
michael-weinstein/figaro2
Long-awaited update for Figaro
michael-weinstein/w32-rps-Spring2024
Repo for the Spring 2024 Git and Docker class
michael-weinstein/W32-git-docker-example
Example repo for UCLA Collaboratory Workshop 32 on Github and Docker
michael-weinstein/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.
michael-weinstein/figaro
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
michael-weinstein/w32-rps-Summer2023
Teaching repo for BIG Summer 2023
michael-weinstein/Azimuth
Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency
michael-weinstein/bigGMaestro
Repo for assisting on CRISPR project
michael-weinstein/bigSummer2022
Rosalind Problems for BIG 2022
michael-weinstein/bootstrapWithOutlier
Statistical demo for question that was asked
michael-weinstein/w32_rps_spring2023
Repo for fall 2022 collaboratory github and docker class
michael-weinstein/bigSummer2024PythonWorkshop2
Big Summer 2024 Example Code
michael-weinstein/color_chart
michael-weinstein/easyMultiprocessing
Easy multiprocessing tool for when multiprocessing should be easy. Demo for OCPython group April 2018.
michael-weinstein/Elevation
End-to-end guide design for CRISPR/Cas9 with machine learning
michael-weinstein/informaticsChallenge092019
Informatics challenge answer submission
michael-weinstein/katacoda-scenarios
Katacoda Scenarios
michael-weinstein/mara
aMino Acid Reversing Application
michael-weinstein/miqScore16SPublic
Repo for public-facing 16s miq score
michael-weinstein/miqScoreGutStandardShotgun
Public repo for the MIQ score system for analyzing Zymo Gut Standard reads
michael-weinstein/miqScoreNGSReadCountPublic
Public repo for miq scoring package for NGS reads
michael-weinstein/miqScoreShotgunPublic
Repo for public-facing shotgun MIQ score
michael-weinstein/miqScoreShotgunPublicSupport
Support package for MIQ score calculation and reporting on untargeted reads.
michael-weinstein/sc2-illumina-pipeline
Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
michael-weinstein/thefirehose
Utility for stress testing of sites that take emails and passwords. Ideal for stress testing of your phishing page. Maybe even someone else's phishing page... although I cannot condone such activity (legally).
michael-weinstein/TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
michael-weinstein/veraT
Generic pipeline for running genomics tools on hoffman. Building workflows in python instead of through the queue.
michael-weinstein/w32-rps-Fall2023
michael-weinstein/w32-rps-fall22
Repo for fall 2022 collaboratory github and docker class
michael-weinstein/zymoTransmit
Python script to facilitate uploading COVID-19 test results to departments of health