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    22 repositories

    • TEbenchmarking

      Public
      Benchmarking computational tools for locus-specific analysis of transposable elements in single-cell RNA-seq datasets
      Jupyter Notebook
      •
      MIT License
      •5•7•0•0•Updated Aug 11, 2026Aug 11, 2026

    • CIARA

      Public
      CIARA (Cluster Independent Algorithm for the identification of markers of RAre cell types) is an R package that identifies potential markers of rare cell types…
      open-sourcefeature-selectioncluster-analysis
      open-sourcefeature-selectioncluster-analysisbioinformatics-analysisrstats-packagerare-cells
      R
      •2•18•1•0•Updated Jan 1, 2026Jan 1, 2026

    • Reevaluating-GRN-inference

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • h3k4me3_maintenance

      Public
      HTML
      •0•0•0•0•Updated Nov 21, 2025Nov 21, 2025

    • scXen

      Public
      Analysis of scRNA-seq data from nuclear transfer Xenopus embryos
      Jupyter Notebook
      •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

    • STREAMLINE

      Public
      STREAMLINE (Topological benchmarking of GRN inference from scRNA-Sequencing data)
      HTML
      •0•8•0•0•Updated Jun 6, 2024Jun 6, 2024

    • scAVE

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Mar 18, 2024Mar 18, 2024

    • Reprogramming-cell-fate---Ding-Yang

      Public
      The code and data that used in the intern. The aim of the internship is to find whether the boundaries in blastula cells change after nucleus transfer.
      0•0•0•0•Updated Nov 9, 2023Nov 9, 2023

    • MATACseq

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 18, 2023Oct 18, 2023

    • human-gastrula-shiny

      Public
      R
      •1•4•2•0•Updated Apr 3, 2023Apr 3, 2023

    • CIARA_python

      Public
      Implementation of entropy of mixing algorithm in python
      opensourcebioinformaticsrna-seq
      opensourcebioinformaticsrna-seqfeature-selectionrna-seq-analysisbioinformatics-analysisbioinformatics-algorithmsbioinformatics-toolcelltype-annotation
      Jupyter Notebook
      •
      MIT License
      •1•10•0•0•Updated Oct 19, 2022Oct 19, 2022

    • WOTPLY

      Public
      R
      •1•2•0•0•Updated Oct 6, 2022Oct 6, 2022

    • 2DLEGI

      Public
      Impact of size and geometry of 2D epithelial tissues on the precision of gradient sensing via nearest-neighbour or long-range intercellular communication
      Jupyter Notebook
      •0•1•0•0•Updated Jun 29, 2022Jun 29, 2022

    • MitoHEAR

      Public
      MitoHEAR (Mitochondrial HEteroplasmy AnalyzeR) is an R package that allows the estimation as well as downstream statistical analysis of the mtDNA heteroplasmy c…
      open-sourcebioinformatics-analysisheteroplasmy
      open-sourcebioinformatics-analysisheteroplasmyrstats-package
      R
      •
      GNU General Public License v3.0
      •3•3•0•0•Updated Jun 2, 2022Jun 2, 2022

    • scanpy

      Public
      Single-cell analysis in Python. Scales to >1M cells.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •763•0•0•0•Updated Mar 28, 2022Mar 28, 2022

    • seurat-wrappers

      Public
      Community-provided extensions to Seurat
      R
      •
      GNU General Public License v3.0
      •145•0•0•0•Updated Mar 16, 2022Mar 16, 2022

    • Spatial-Transcriptomics

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 11, 2022Feb 11, 2022

    • gastrula_code

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 3, 2022Feb 3, 2022

    • GRANpy

      Public
      Graph Auto-Encoders (GAE) for Gene Regulatory Network (GRN) completion using scRNA-Seq datasets
      Python
      •
      MIT License
      •353•2•0•0•Updated Jan 19, 2022Jan 19, 2022

    • DiffVAE

      Public
      Code for Nature Scientific Reports 2020 paper: "Unsupervised generative and graph neural methods for modelling cell differentiation" by Ioana Bica, Helena André…
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Jul 9, 2021Jul 9, 2021

    • Cell-Competition-Paper-Figures

      Public
      HTML
      •0•0•0•0•Updated Jul 2, 2021Jul 2, 2021

    • COMUNET

      Public template
      COMUNET: a tool to explore and visualize intercellular communication
      Jupyter Notebook
      •9•13•2•0•Updated Apr 15, 2020Apr 15, 2020
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