RV144: source code

List of figures:

Fig. 2, Fig. 3, Fig. 4, Fig. 5, Fig. 6

Fig. 2

Fig. 2: R code [MD], Input file [RData]

Fig. 3

Fig. 3: R code [MD], Input file [RData]

Fig. 4

Fig. 4: R code [MD]

Fig. 5

Fig. 6

Supplemental material:

a. transcriptomic pilot study:

code:

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

input:

• non-normalized matrix: [[CSV]](see data release)
• arrays/samples annotation: [CSV]
• features annotation: [TSV]

output:

• non-normalized ExpressionSet: [RDA]
• quantile normalized ExpressionSet: [RDA]
• DMSO-substracted ExpressionSet: [RDA]
• pre-vaccination-substracted ExpressionSet: [RDA]
• MArrayLM list: [RDA]
• gsea result table: [RDA]
• slea ExpressionSet: [RDA]

b. transcriptomic case/control study:

code:

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

input:

• non-normalized matrix: [[CSV]](see data release)
• arrays/samples annotation: [CSV]
• features annotation: [TSV]
• antibody and cellular data: [CSV]
• flow cytometry data: counts [CSV], population annotation [CSV], sample annotation [CSV]
• luminex data: [CSV]
• ics data: [CSV]
• haplotype data: [CSV]

output:

• non-normalized ExpressionSet: [RDA]
• quantile normalized ExpressionSet: [RDA]
• DMSO-substracted ExpressionSet: [RDA]
• MArrayLM list: [RDA]
• gsea result table: [RDA]
• slea ExpressionSet: [RDA]
• antibody and cellular ExpressionSet: [RDA]
• flow cytometry ExpressionSet: raw [RDA], normalized [RDA]
• luminex ExpressionSet: [RDA]
• ics ExpressionSet: [RDA]
• haplotype ExpressionSet: [RDA]