R code to reproduce the transcriptomic analysis of the Dias/Koup project

Fig. 6A-B, Fig. 6C

Fig. 6A-B: R code [MD]

Fig. 6C: R code [MD]

code:

• preprocessing: [MD]
• genesets enrichment analysis: [MD]

input:

• non-normalized (raw) gene counts: [CSV]
• Rhesus genome annotation (see data release)
• alignment statistics: [TSV]
• sample annotation: [XLSX]
• viral load and bnAb concentrations: [XLSX]

output:

• raw SeqExpressionSet: [RDA]
• normalized SeqExpressionSet: [RDA]
• baseline-substracted SeqExpressionSet: [RDA]
• DGEGLM list: [RDA]
• GSEA output (see data release)

code:

• preprocessing: [MD]

input:

• non-normalized (raw) gene counts: [CSV]
• Rhesus genome annotation (see data release)
• alignment statistics: [TSV]
• sample annotation: [XLSX], [TSV]

output:

• raw SeqExpressionSet: [RDA]
• normalized SeqExpressionSet: [RDA]
• baseline-substracted SeqExpressionSet: [RDA]
• DGEGLM list (see data release)
• fGSEA output (see data release)