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    32 repositories

    • 2026_Pneumonia_endotypes

      Public
      Code for “Pathogen-specific host responses define distinct pneumonia endotypes in the human lung” manuscript
      Jupyter Notebook
      •0•0•0•0•Updated Jun 22, 2026Jun 22, 2026

    • Guggilla_Matsuda_Auxora_2026

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 18, 2026May 18, 2026

    • utils

      Public
      Collection of useful scripts, largely for sequence analysis
      Jupyter Notebook
      •5•7•5•0•Updated May 13, 2026May 13, 2026

    • sc_utils

      Public
      Python
      •0•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • Thayer_2026

      Public
      Code for analysis and figures, A single-cell atlas of mouse and human spleen identifies white pulp macrophage ontogeny and changes during aging , Thayer 2026
      Jupyter Notebook
      •0•1•2•0•Updated Apr 8, 2026Apr 8, 2026

    • 2026_Grant

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • CarpeDiemCLAD

      Public
      Code for the CLAD version of the CarpeDiem data browser
      JavaScript
      •1•0•0•0•Updated Nov 4, 2025Nov 4, 2025

    • 2025_Markov_SSc

      Public
      Code for ”Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease“
      Jupyter Notebook
      •0•0•0•0•Updated Oct 8, 2025Oct 8, 2025

    • SScILD-EHR-M1

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • Bailey_Puritz_Senkow_RPRA_2024

      Public
      Code base for Bailey, Puritz, Senkow, et al. (2024) "Profibrotic monocyte-derived alveolar macrophages are expanded in patients with persistent respiratory symp…
      Jupyter Notebook
      •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

    • 2024_Fenske_Peltekian

      Public
      Jupyter Notebook
      •1•3•0•0•Updated Oct 4, 2024Oct 4, 2024

    • 2024_Markov_Ren_Senkow

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Aug 13, 2024Aug 13, 2024

    • 2023_Grant_Poor

      Public
      Public respository for the manuscript: "Prolonged exposure to lung-derived cytokines is associated with inflammatory activation of microglia in patients with CO…
      R
      •
      MIT License
      •0•1•0•0•Updated May 24, 2024May 24, 2024

    • seqextendeR

      Public
      A collection of tools and extensions for bulk and single-cell RNA-seq analysis
      R
      •
      MIT License
      •0•0•0•0•Updated May 9, 2024May 9, 2024

    • which_genome

      Public
      Identify genome build from a list of genes
      Python
      •
      MIT License
      •0•2•0•0•Updated Sep 7, 2023Sep 7, 2023

    • nupulmonary.org

      Public
      Our website
      HTML
      •1•0•0•0•Updated Aug 1, 2023Aug 1, 2023

    • 2020_Grant

      Public
      Code base for the Grant, Morales-Nebreda, and Markov et al., “Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia” Nature (2021) paper
      biologysequencingflow-cytometry
      biologysequencingflow-cytometrysingle-cell-rna-seqbulk-rna-seqcovid-19
      Jupyter Notebook
      •4•8•0•0•Updated Jul 18, 2023Jul 18, 2023

    • stoeger_et_al_2022_transcriptome_imbalance

      Public
      Code accompanying manuscript
      Jupyter Notebook
      •2•7•0•0•Updated Oct 14, 2022Oct 14, 2022

    • 2021_Koch

      Public
      R
      •0•2•0•0•Updated Oct 25, 2021Oct 25, 2021

    • scanpy-utils

      Public
      Utility functions for scanpy
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 11, 2021Aug 11, 2021

    • 2021_CF_ACE2

      Public
      HTML
      •0•1•0•0•Updated Jul 27, 2021Jul 27, 2021

    • 2021_Watanabe

      Public
      Repository to accompany “Resetting proteostasis with ISRIB promotes epithelial differentiation to attenuate pulmonary fibrosis” Watanabe et al. manuscript
      Python
      •0•0•0•0•Updated May 11, 2021May 11, 2021

    • infohub

      Public
      0•0•0•0•Updated Apr 2, 2021Apr 2, 2021

    • 2020_MoralesNebreda

      Public
      0•0•0•0•Updated Feb 18, 2021Feb 18, 2021

    • JoshiWatanabe2019

      Public
      HTML
      •2•2•0•0•Updated Dec 22, 2020Dec 22, 2020

    • 2020_Bharat

      Public
      Analysis accompanying Bharat et al., 2020 manuscript
      Jupyter Notebook
      •2•2•1•0•Updated Nov 30, 2020Nov 30, 2020

    • Doublehit_Human_scRNA_Analysis

      Public
      Codes and analysis workflow for integrating human scRNA-seq data from six different studies to reveal age-related signatures.
      R
      •
      MIT License
      •1•4•0•0•Updated Oct 26, 2020Oct 26, 2020

    • scarches-covid-reference

      Public
      Build a reference model for COVID-positive BAL fluid scRNA-seq samples from Grant et al., 2020 with scArches
      Jupyter Notebook
      •0•7•0•0•Updated Sep 7, 2020Sep 7, 2020

    • 2019_Strunz

      Public
      Reproducibility repo accompanying Angelidis et al. "Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration"
      Jupyter Notebook
      •10•0•0•0•Updated Apr 25, 2020Apr 25, 2020

    • rootstock

      Public
      Clone me to create your Manubot manuscript
      HTML
      •
      Other
      •192•0•0•0•Updated Jun 28, 2019Jun 28, 2019
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