Stars
This is the alpha version of the CellOracle package
UCE is a zero-shot foundation model for single-cell gene expression data
dpeerlab / wishbone
Forked from ManuSetty/wishboneWishbone is an algorithm to align cells along developmental trajectories with branches
BIA Bob is a Jupyter+LLM-based assistant for interacting with image data and for working on Bio-image Analysis tasks.
A causal implicit generative model for simulating single-cell RNA-seq data guided by a gene regulatory network 🧬
A collection of web applications for exploring single cell RNA-seq data
Chat with your database or your datalake (SQL, CSV, parquet). PandasAI makes data analysis conversational using LLMs and RAG.
A python function to calculate the fractal dimension in 3D.
Sema7A guides lateral line sensory arbors
Fastest Gephi's ForceAtlas2 graph layout algorithm implemented for Python and NetworkX
Depicting pseudotime-lagged causality for accurate gene-regulatory inference
A Python nearest neighbor descent for approximate nearest neighbors
Publication Page for Satpathy*, Granja* et al 2019
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
A simulator for single-cell expression data guided by gene regulatory networks
covolutional neural network based coexpression analysis
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
BEELINE: evaluation of algorithms for gene regulatory network inference
This repository contains all scripts needed to reproduce figures from: Kozak et al., "Epithelial planar bipolarity emerges from Notch-mediated asymmetric inhibition of Emx2", Current Biology, 2019