shangshanzhizhe

generative-ai-for-beginners

18 Lessons, Get Started Building with Generative AI 🔗 https://microsoft.github.io/generative-ai-for-beginners/

python-fire

Python Fire is a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.

LazyVim

Neovim config for the lazy

emoji-cheat-sheet

A markdown version emoji cheat sheet

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

Awesome-GPT-Agents

A curated list of GPT agents for cybersecurity

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

SAIGE

MoMAColors

Color Schemes based around artwork and the Museum of Modern Art.

blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

gqt

A genotype query interface.

NECAT

Nanopore data assembler

ggsashimi

Command-line tool for the visualization of splicing events across multiple samples

regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

StainedGlass

Make colorful identity heatmaps of genomic sequence

local_pca

Methods for examining PCA locally along the genome.

snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

unialigner

SAIGE

Development for SAIGE and SAIGE-GENE(+)

smoothxg

linearize and simplify variation graphs using blocked partial order alignment

vechat

Correcting errors in noisy long reads using variation graphs

FRASER

FRASER - Find RAre Splicing Events in RNA-seq

TEspeX

TEspeX - pipeline for Transposable Elements expression quantification

FastCall

Super fast variant caller for whole genome shotgun (WGS) sequencing data

lostruct-py

pman_inversions

Scripts associated with Harringmeyer & Hoekstra, 2022