FluOMICS lung: source code

List of figures:

Fig. 1A, Fig. 1D, Fig. 2A, Fig. 2B, Fig. 2C, Fig. 2D, Fig. 2H, Fig. 2J

Fig. 1A

Fig. 1A: R code [MD], Input file [RDA]

Fig. 1D

Fig. 1D: R code [MD], Input files [RDA]

Fig. 2A

Fig. 2A: R code [MD], Input files [RDA]

Fig. 2B

Fig. 2B: R code [MD], Input files [TSV]

Fig. 2C

Fig. 2C: R code [MD]

Fig. 2D

Fig. 2D: R code [MD]

Fig. 2H

Fig. 2H: R code [MD], Input files [RDA]

Fig. 2J

Fig. 2J: R code [MD]

Supplemental material:

a. RNA-Seq analysis:

code:

• preprocessing: [MD]
• geneset-analysis: [MD]

input:

• non-normalized (raw) gene counts: [CSV]
• mouse GRCm38 genome annotation: [GTF]
• sample annotation: [TSV]

output:

• raw SeqExpressionSet: [RDA]
• normalized SeqExpressionSet: [RDA]
• mock-subtracted SeqExpressionSet: [RDA]
• DGEGLM list: [RDA]
• gsea results table: [RDA]

b. Genesets differentiating between Mo-derived and tissue-residents macrophages:

code:

• gmt creation: [MD]

output:

• macrophage origin gmt: [TSV]

c. Web-scrapping of the interferome data

code:

• gmt creation: [MD]

output:

• interferome gmt: [TSV]