JAEKYUNG SHIN's repositories
matplotlib
matplotlib: plotting with Python
adversarial
Code and hyperparameters for the paper "Generative Adversarial Networks"
celfie
cfDNA cell type of origin estimation
cell2location
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
cell2location_paper-Fig-2H-
Cell2location paper - Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics
dataviz
A book covering the fundamentals of data visualization
dorothea
R package to access DoRothEA's regulons
liana
LIANA: a LIgand-receptor ANalysis frAmework
nichenetr
NicheNet: predict active ligand-target links between interacting cells
ocean
R package for metabolic enzyme enrichment anaylsis
OmnipathR
R client for the OmniPath web service
scrattch
Single cell RNA-seq analysis for transcriptomic type characterization
scrattch.bigcat
iterative clustering pipeline of big single cell datasets.
scrattch.hicat
Hierarchical, iterative clustering for analysis of transcriptomics data in R
scvelo
RNA Velocity generalized through dynamical modeling
scvi-tools
Deep probabilistic analysis of single-cell omics data
SEARCHIN
Systematic Elucidation and Assessment of Regulatory Cell-to-cell Interaction Networks (SEARCHIN)
SingleR
SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
stitching-spark
Reconstruct big images from overlapping tiled images on a Spark cluster.
strelka
Strelka2 germline and somatic small variant caller
tidyseurat
Seurat meets tidyverse. The best of both worlds.
transcriptutorial
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
uwot
An R package implementing the UMAP dimensionality reduction method.