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    16 repositories

    • cellpose

      Public
      a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •415•4•2•0•Updated Oct 5, 2024Oct 5, 2024

    • velocity_package

      Public template
      Python
      •
      GNU Affero General Public License v3.0
      •2•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • Tex_repro

      Public
      Jupyter notebooks for reproducing the results of Gupta et al. 2024
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

    • MORESCA

      Public
      This repository provides a template and some resources on standardized scRNA-seq analysis using Python.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•20•1•Updated Jan 23, 2024Jan 23, 2024

    • pyPsupertime

      Public
      Scalable reimplementation of psupertime in python
      Python
      •
      MIT License
      •0•1•1•0•Updated Sep 29, 2023Sep 29, 2023

    • cytopath

      Public
      Simulation based inference of differentiation trajectories from RNA velocity fields.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•0•0•Updated Aug 22, 2023Aug 22, 2023

    • S3-CIMA

      Public
      Supervised Spatial Single-Cell Image Analysis
      Jupyter Notebook
      •1•2•1•0•Updated Jul 28, 2023Jul 28, 2023

    • Teamproject-2023

      Public
      Implementation of RNA velocity for estimation of single cell transcriptomic dynamics.
      visualizationbioinformaticsrna-seq-analysis
      Python
      •0•0•25•0•Updated Jul 25, 2023Jul 25, 2023

    • DICSIT

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Dec 23, 2022Dec 23, 2022

    • MoESimVAE

      Public
      Mixture-of-Experts Variational Autoencoder for Clustering and Generating from Similarity-Based Representations on Single Cell Data
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Apr 22, 2021Apr 22, 2021

    • CellCnn

      Public
      Representation Learning for detection of phenotype-associated cell subsets
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •28•0•0•0•Updated Oct 24, 2020Oct 24, 2020

    • psupertime

      Public
      psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
      R
      •
      GNU General Public License v3.0
      •13•0•0•0•Updated Jul 8, 2020Jul 8, 2020

    • gleason_CNN

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •17•0•0•0•Updated Jul 27, 2019Jul 27, 2019

    • TreeTop

      Public
      TreeTop is an algorithm for single-cell data analysis to identify and assess statistical significance of branch points in biological processes with possibly multi-level branching hierarchies. We demonstrate branch point identification for processes with varying topologies, including T cell maturation, B cell differentiation and hematopoiesis. Ou…
      MATLAB
      •2•0•0•0•Updated Jan 29, 2019Jan 29, 2019

    • STILT

      Public
      Stochastic Inference on Lineage Trees
      C++
      •1•0•0•0•Updated Jan 6, 2017Jan 6, 2017

    • matLeap

      Public
      matLeap: A fast adaptive Matlab-ready tau-leaping implementation suitable for Bayesian inference
      C++
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 12, 2016Oct 12, 2016