abnomic: antibody profile immunomics project

The goal of abnomic is to provide a reproducible workflow for the undergraduate thesis project: “Comparación de la respuesta de anticuerpos ante Plasmodium vivax en pacientes de la Amazonía Peruana según su severidad y episodios previos mediante microarreglos de proteínas”.

Outputs

• take a look at the approved project

To-Do

• ( ) create a renv environment

Reproducibility

Dataset required:

• for 03-sevrcov.Rmd
  • data-raw/malaria severa 28Nov2014_Ed.dta
  • data-raw/severe_malaria_vivax SEP2016.dta
  • data-raw/samples.csv
• for 04-abnomic.Rmd
  • data-raw/ADi-NAMRU6_Data-samples.csv
  • data-raw/samples.csv
  • data-raw/PfPv500_NonpresentReactiveTargets.xlsx
• for 04-abnomic.Rmd generated after PlasmoDB strategy
  • data/04-listgen.tsv
  • data/04-listall.tsv
  • data/04-listgit.tsv
  • data/00-protn6c.xlsx
  • data/00-protn6c.xlsx

plasmodb search strategy

whole genome

• link: https://plasmodb.org/plasmo/app/workspace/strategies/import/1247ea53c4a464a3
• local route: data/20211013-02_whole_31ago2017-pvx_genome.txt
• characteristics:
  • 5665 genes
• variables:
  • Gene ID
  • Transcript ID
  • Product description
  • Gene name or symbol

all genes by ID in microarray chip

• link: https://plasmodb.org/plasmo/app/workspace/strategies/import/b32a1aefa2a27bbd
• local route: data/20211013-01_allgen_20ago2017-microarray_chip.txt
• characteristics:
  • 873 genes
  • 880 transcripts
• variables:
  • Same as previous, plus
  • Ortholog count
  • Gene variability (Total SNPs, NonSyn/Syn SNP ratio)
  • Protein extracellular localization and secretory pathways (# TM domains, SignalP scores)
  • Gene ontology (components, functions, processes)
  • Gene characteristics (# exons and transcripts, length of transcript, CDS and protein)