Yinuo Jin's repositories
Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
cell2loc_simulate
Cell2location paper - Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics
cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
DMT_loss
DMT codes for the ICLR 2021 paper: Topology-Aware Segmentation Using Discrete Morse Theory
dynamicTreeCut
Python translation of the hybrid dynamicTreeCut method as created by Peter Langfelder and Bin Zhang.
intro-numerical-methods
Jupyter notebooks and other materials developed for the Columbia course APMA 4300
nichenetr
NicheNet: predict active ligand-target links between interacting cells
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
scvi-tools
Deep probabilistic analysis of single-cell omics data
splatter
Simple simulation of single-cell RNA sequencing data
starfysh
Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
statannotations
add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction