Jayoung Kim Ryu's repositories
anndata
Annotated data matrices.
Batch-effect-removal-benchmarking
A benchmark of batch-effect correction methods for single-cell RNA sequencing data
bsub_jupyter
Connect to a LSF main node directly or trough a ssh jump node, launch a jupyter notebook via bsub and open automatically a tunnel. The name of the connection can be used to reestablish the connection later or to terminate it.
climate-viz
Creating climate change visualizations
CRISPResso2
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
fit_nbinom
Negative binomial maximum likelihood estimate implementation in Python using L-BFGS-B
jykr.github.io
Personal Blog using Hydeout
mageck-1
Experimental source code for MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout)
manta
Structural variant and indel caller for mapped sequencing data
mlcrate
A python module of handy tools and functions, mainly for ML and Kaggle
mudata
Multimodal Data (.h5mu) implementation for Python
perturb-tools
Analysis Framework for Pooled CRISPR Genome Editing Screens
POT
POT : Python Optimal Transport
pyro-ppl
Deep universal probabilistic programming with Python and PyTorch
PyTorch-BigGraph
Generate embeddings from large-scale graph-structured data.
pytorch_geometric
Graph Neural Network Library for PyTorch
simba_tutorials
Tutorials for SIMBA (https://github.com/pinellolab/simba)
vectorizers
Vectorizers for a range of different data types