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1. 2020_Grant 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

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2. scarches-covid-reference scarches-covid-reference Public

   Build a reference model for COVID-positive BAL fluid scRNA-seq samples from Grant et al., 2020 with scArches

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3. stoeger_et_al_2022_transcriptome_imbalance stoeger_et_al_2022_transcriptome_imbalance Public

   Code accompanying manuscript

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4. Reyfman2018 Reyfman2018 Public

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

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5. utils utils Public

   Collection of useful scripts, largely for sequence analysis

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6. Doublehit_Human_scRNA_Analysis Doublehit_Human_scRNA_Analysis Public

   Codes and analysis workflow for integrating human scRNA-seq data from six different studies to reveal age-related signatures.

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