jykr
Bioinformatics & Integrative Genomics Ph.D. candidate at Harvard & MGH
Harvard Medical School, @pinellolab Boston, MA
Pinned Repositories
Perturb-OT
Cross-modality matching and prediction with labeled Gromov-Wasserstein Optimal Transport.
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
crispr-bean
Base Editing screens' Activity-Normalized variant effect size estimation
simba
SIMBA: SIngle-cell eMBedding Along with features
simba_pbg
A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraph
jykr's Repositories
jykr/anndata
Annotated data matrices.
jykr/Batch-effect-removal-benchmarking
A benchmark of batch-effect correction methods for single-cell RNA sequencing data
jykr/be_predict_efficiency
jykr/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.
jykr/climate-viz
Creating climate change visualizations
jykr/CRISPResso2
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
jykr/fit_nbinom
Negative binomial maximum likelihood estimate implementation in Python using L-BFGS-B
jykr/jykr
Config files for my GitHub profile.
jykr/jykr.github.io
Personal Blog using Hydeout
jykr/ldsc-sparse
Stratified LD Score Regression (S-LDSC) for sparse annotation
jykr/mageck-1
Experimental source code for MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout)
jykr/manta
Structural variant and indel caller for mapped sequencing data
jykr/mlcrate
A python module of handy tools and functions, mainly for ML and Kaggle
jykr/mudata
Multimodal Data (.h5mu) implementation for Python
jykr/perturb-tools
Analysis Framework for Pooled CRISPR Genome Editing Screens
jykr/POT
POT : Python Optimal Transport
jykr/pyro-ppl
Deep universal probabilistic programming with Python and PyTorch
jykr/PyTorch-BigGraph
Generate embeddings from large-scale graph-structured data.
jykr/pytorch_geometric
Graph Neural Network Library for PyTorch
jykr/simba_tutorials
Tutorials for SIMBA (https://github.com/pinellolab/simba)
jykr/SpatialDE2_Normal
Test genes for Spatial Variation
jykr/svutils
Some useful scripts to process structural variant calls
jykr/vectorizers
Vectorizers for a range of different data types