Pinned Repositories
2020_Grant
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
2021_Koch
2024_Markov_Ren_Senkow
Doublehit_Human_scRNA_Analysis
Codes and analysis workflow for integrating human scRNA-seq data from six different studies to reveal age-related signatures.
JoshiWatanabe2019
Reyfman2018
This repository contains R code used to analyze bulk and single-cell RNA-seq data published in Reyfman et al., AJRCCM, 2018.
scarches-covid-reference
Build a reference model for COVID-positive BAL fluid scRNA-seq samples from Grant et al., 2020 with scArches
stoeger_et_al_2022_transcriptome_imbalance
Code accompanying manuscript
utils
Collection of useful scripts, largely for sequence analysis
which_genome
Identify genome build from a list of genes
NU Pulmonary's Repositories
NUPulmonary/2020_Grant
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
NUPulmonary/scarches-covid-reference
Build a reference model for COVID-positive BAL fluid scRNA-seq samples from Grant et al., 2020 with scArches
NUPulmonary/stoeger_et_al_2022_transcriptome_imbalance
Code accompanying manuscript
NUPulmonary/Reyfman2018
This repository contains R code used to analyze bulk and single-cell RNA-seq data published in Reyfman et al., AJRCCM, 2018.
NUPulmonary/utils
Collection of useful scripts, largely for sequence analysis
NUPulmonary/Doublehit_Human_scRNA_Analysis
Codes and analysis workflow for integrating human scRNA-seq data from six different studies to reveal age-related signatures.
NUPulmonary/2021_Koch
NUPulmonary/2024_Markov_Ren_Senkow
NUPulmonary/JoshiWatanabe2019
NUPulmonary/which_genome
Identify genome build from a list of genes
NUPulmonary/2020_Bharat
Analysis accompanying Bharat et al., 2020 manuscript
NUPulmonary/2021_CF_ACE2
NUPulmonary/2023_Grant_Poor
Public respository for the manuscript: "Prolonged exposure to lung-derived cytokines is associated with inflammatory activation of microglia in patients with COVID-19
NUPulmonary/2024_Fenske_Peltekian
NUPulmonary/Bailey_Puritz_Senkow_RPRA_2024
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"
NUPulmonary/2019_Strunz
Reproducibility repo accompanying Angelidis et al. "Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration"
NUPulmonary/2020_MoralesNebreda
NUPulmonary/2021_Watanabe
Repository to accompany “Resetting proteostasis with ISRIB promotes epithelial differentiation to attenuate pulmonary fibrosis” Watanabe et al. manuscript
NUPulmonary/Budinger-Lab
Pulmonary and Critical Care in the Department of Medicine at Northwestern University
NUPulmonary/infohub
NUPulmonary/nupulmonary.org
Our website
NUPulmonary/rootstock
Clone me to create your Manubot manuscript
NUPulmonary/scanpy-utils
Utility functions for scanpy
NUPulmonary/seqextendeR
A collection of tools and extensions for bulk and single-cell RNA-seq analysis