REAGENT or RESOURCE	SOURCE	IDENTIFIER
Software and algorithms
DESeq2	Love et al., 201462	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Limma	Ritchie et al., 201563	http://bioconductor.org/packages/release/bioc/html/limma.html
EnhancedVolcano	Blighe et al., 202364	http://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
ComplexHeatmap	Gu et al., 201665	https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
ggplot2	Wickham., 201666	https://ggplot2.tidyverse.org/
ggfortify	Tang et al. 201667	https://cran.r-project.org/web/packages/ggfortify/index.html
Survival	Therneau et al. 200068	https://cran.r-project.org/web/packages/survival/index.html
Seurat	Hao and Hao et al. 202169	https://satijalab.org/seurat/index.html
GSDecon		https://github.com/JasonHackney/GSDecon/
FGSEA	Korotkevich et al., 201970	https://bioconductor.org/packages/release/bioc/html/fgsea.html
DropletUtils	Lun et al., 201971	https://bioconductor.org/packages/release/bioc/html/DropletUtils.html
scater	McCarthy et al., 201782	https://bioconductor.org/packages/release/bioc/html/scater.html
survminer	Kassambara et al., 202273	https://cran.r-project.org/web/packages/survminer/index.html
forestplot	Gordon et al., 202272	https://cran.r-project.org/web/packages/forestplot/index.html
ROCR	Sing et al., 202074	https://cran.r-project.org/web/packages/ROCR/index.html
cellranger	Zheng et al., 201775	https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome
kallisto	Bray et al., 201676	http://pachterlab.github.io/kallisto/download.html
scanpy	Wolf et al., 201877	https://github.com/theislab/Scanpy
gsnap	Lawrence et al., 201378	https://bioconductor.org/packages/release/bioc/html/gmapR.html
summarizeOverlaps	Lawrence et al. 201378	https://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html
ENSEMBL	Ensembl	http://jan2020.archive.ensembl.org/Homo_sapiens/Info/Index
Deposited data
COVACTA RNA-seq and Olink	Shivram et al., 202314	EGA: EGAS00001006688
Human monocyte stimulation with IL-6 in vitro	This paper	GEO: GSE234002
COVID-19 PBMC and whole blood single cell RNA-seq	Schulte-Schrepping et al. 202011	http://fastgenomics.org
COVID-19 BAL scRNA-seq	Liao et al. 20207	SRA: PRJNA608742
COVID-19 whole blood scRNA-seq	Silvin et al. 202012	ArrayExpress: E-MTAB-9221
COVID-19 lung biopsy scRNA-seq	Delorey et al. 20215	GEO: GSE162911
COVID-19 BAL scRNA-seq	Grant et al. 20216	GEO: GSE155249
COMET whole blood scRNA-seq	Combes et al. 20212	GEO: GSE163668
COMET PBMC scRNA-seq	van der Wijst et al. 202139	GEO: GSE168453
COMET endotracheal aspirate scRNA-seq	Sarma et al. 202138	GEO: GSE163426