home: http://mybic.chop.edu/labs/falkm/gas1_antioxidant_drugs
output: /nas/is1/zhangz/projects/falk/2015-01_Worm_Antioxidant_Drugs/results/pairwise
input:
  anno: /nas/is1/zhangz/projects/falk/2015-01_Worm_Antioxidant_Drugs/R/anno_url.rds
  expr: /nas/is1/zhangz/projects/falk/2015-01_Worm_Antioxidant_Drugs/R/expr75_adjuted.rds
  geneset: /nas/is1/rchive/data/gene.set/r/default_set_worm_5-1000.rds
  template: https://raw.githubusercontent.com/zhezhangsh/DEGandMore/master/examples/DeReport/DeReport.Rmd
  remote: yes
  genome: worm
  paired: no
  penalty: 0.6
  comparison:
    MS010_L1:
    - MS010_L1_49
    - MS010_L1_57
    - MS010_L1_65
    - MS010_L1_73
    dTPP_L1:
    - dTPP_L1_51
    - dTPP_L1_59
    - dTPP_L1_67
    - dTPP_L1_75
  deg:
    method: DeRankP
    cutoff.l2r: 0.0e+00
    cutoff.p: 0.05
    cutoff.fdr: 0.05
    num.top: 250.0
    nperm: 100.0
    logged: yes
  gsea:
    jar: /nas/is1/rchive/data/gene.set/gmt/gsea2-2.2.0.jar
    preranked: no
    thread: 1
    template: https://raw.githubusercontent.com/zhezhangsh/DEGandMore/master/examples/gsea/GSEA_example.yaml
    remote: yes
    kegg: /nas/is1/rchive/data/pathway/public/kegg/src
    gmt:
      GO_BP: /nas/is1/rchive/data/gene.set/gmt/worm/BioSystems/GO_BP.gmt
      GO_MF: /nas/is1/rchive/data/gene.set/gmt/worm/BioSystems/GO_MF.gmt
      GO_CC: /nas/is1/rchive/data/gene.set/gmt/worm/BioSystems/GO_CC.gmt
      OMIM_gene: /nas/is1/rchive/data/gene.set/gmt/worm/OMIM/OMIM_gene.gmt
      MSigDb_Hallmark: /nas/is1/rchive/data/gene.set/gmt/worm/MSigDb/C0_Hallmark.gmt
      MSigDb_Positional: /nas/is1/rchive/data/gene.set/gmt/worm/MSigDb/C1_Positional.gmt
      MsigDb_Chemical_and_genetic_perturbations: /nas/is1/rchive/data/gene.set/gmt/worm/MSigDb/C2_Chemical_and_genetic_perturbations.gmt
      MSigDb_MicroRNA_targets: /nas/is1/rchive/data/gene.set/gmt/worm/MSigDb/C3_MicroRNA_targets.gmt
      MSigDb_TF_targets: /nas/is1/rchive/data/gene.set/gmt/worm/MSigDb/C3_TF_targets.gmt
      MSigDb_Oncogenic_signatures: /nas/is1/rchive/data/gene.set/gmt/worm/MSigDb/C6_Oncogenic_signatures.gmt
      MSigDb_Immunologic_signatures: /nas/is1/rchive/data/gene.set/gmt/worm/MSigDb/C7_Immunologic_signatures.gmt
      BioCarta_pathway: /nas/is1/rchive/data/gene.set/gmt/worm/MSigDb/C2_BioCarta_Pathways.gmt
      REACTOME_pathway: /nas/is1/rchive/data/gene.set/gmt/worm/BioSystems/REACTOME.gmt                
      Wiki_pathway: /nas/is1/rchive/data/gene.set/gmt/worm/BioSystems/WikiPathways.gmt                 
      KEGG_pathway: /nas/is1/rchive/data/gene.set/gmt/worm/KEGG/KEGG_pathway.gmt
      KEGG_compound: /nas/is1/rchive/data/gene.set/gmt/worm/KEGG/KEGG_compound.gmt
      KEGG_enzyme: /nas/is1/rchive/data/gene.set/gmt/worm/KEGG/KEGG_enzyme.gmt
      KEGG_module: /nas/is1/rchive/data/gene.set/gmt/worm/KEGG/KEGG_module.gmt
      KEGG_reaction: /nas/is1/rchive/data/gene.set/gmt/worm/KEGG/KEGG_reaction.gmt
project: # Project background
  Title: Treatment of gas-1 mutated C. Elegans with antioxidant drugs ## Project title
  Home: http://mybic.chop.edu/labs/falkm/gas1_antioxidant_drugs ## Project home page
  Description: This project uses gene expression microarray data to study effect of antioxidant drugs on C. Elegans worms with gas-1 mutation. ## Full description