Repositories list

• utils

  Public
  Collection of useful scripts, largely for sequence analysis

  R

  •4•4•5•0•Updated Nov 1, 2024Nov 1, 2024

• 2024_Fenske_Peltekian

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Oct 4, 2024Oct 4, 2024

• 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 symptoms and radiographic abnormalities after COVID-19"

  Jupyter Notebook

  •0•0•0•0•Updated Sep 25, 2024Sep 25, 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 COVID-19

  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+ 3single-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•6•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•1•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•3•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

  •11•0•0•0•Updated Apr 25, 2020Apr 25, 2020

• rootstock

  Public
  Clone me to create your Manubot manuscript

  HTML

  •

  Other

  •177•0•0•0•Updated Jun 28, 2019Jun 28, 2019

• Reyfman2018

  Public
  This repository contains R code used to analyze bulk and single-cell RNA-seq data published in Reyfman et al., AJRCCM, 2018.

  R

  •6•5•0•0•Updated May 24, 2019May 24, 2019

• Budinger-Lab

  Public
  Pulmonary and Critical Care in the Department of Medicine at Northwestern University

  R

  •0•0•0•0•Updated Jun 12, 2017Jun 12, 2017