jykr Goto Github PK

anndata

Annotated data matrices.

batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

be_predict_efficiency

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

Config files for my GitHub profile.

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)

svutils

Some useful scripts to process structural variant calls

vectorizers

Vectorizers for a range of different data types