params_flop.json

{
    "filtering": "unfiltered,filtered",
    "diffexp_pipelines": "vsn_norm limma_analysis,voom_norm limma_analysis,tmm_norm limma_analysis,log2quant_norm limma_analysis,edger_analysis,deseq2_analysis",
    "functional_analysis": "TRUE",
    "flop_ngenes_threshold": "30",
    "flop_pval_threshold": "1",
    "filterbyexpr_libsize": "NULL",
    "filterbyexpr_mincount": "10",
    "filterbyexpr_mintotalcount": "15",
    "filterbyexpr_largen": "10",
    "filterbyexpr_minprop": "0.7",
    "diffexp_limma_ndups": "1",
    "diffexp_limma_spacing": "1",
    "diffexp_limma_block": "NULL",
    "diffexp_limma_weights": "NULL",
    "diffexp_limma_method": "ls",
    "diffexp_deseq2_test": "Wald",
    "diffexp_deseq2_fitType": "parametric",
    "diffexp_deseq2_quiet": "FALSE",
    "diffexp_deseq2_betaprior": "FALSE",
    "diffexp_deseq2_minReplicatesForReplace": "7",
    "diffexp_deseq2_parallel": "FALSE",
    "diffexp_edger_calcnormfactors_method": "TMM",
    "diffexp_edger_calcnormfactors_refColumn": "NULL",
    "diffexp_edger_calcnormfactors_logratiotrim": "0.3",
    "diffexp_edger_calcnormfactors_sumtrim": "0.05",
    "diffexp_edger_calcnormfactors_doweighting": "TRUE",
    "diffexp_edger_calcnormfactors_acutoff": "-1e10",
    "diffexp_edger_calcnormfactors_p": "0.75",
    "diffexp_edger_estimatedisp_priordf": "NULL",
    "diffexp_edger_estimatedisp_trendmethod": "locfit",
    "diffexp_edger_estimatedisp_tagwise": "TRUE",
    "diffexp_edger_estimatedisp_mixeddf": "FALSE",
    "diffexp_edger_estimatedisp_span": "NULL",
    "diffexp_edger_estimatedisp_minrowsum": "5",
    "diffexp_edger_estimatedisp_gridlength": "21",
    "diffexp_edger_estimatedisp_gridrange": "c(-10,10)",
    "diffexp_edger_estimatedisp_robust": "FALSE",
    "diffexp_edger_estimatedisp_winsortailp": "c(0.05, 0.1)",
    "diffexp_edger_estimatedisp_tol": "1e-06",
    "diffexp_edger_glmqlfit_dispersion": "NULL",
    "diffexp_edger_glmqlfit_libsize": "NULL",
    "diffexp_edger_glmqlfit_offset": "NULL",
    "diffexp_edger_glmqlfit_weights": "NULL",
    "diffexp_edger_glmqlfit_abundancetrend": "TRUE",
    "diffexp_edger_glmqlfit_avelogcpm": "NULL",
    "diffexp_edger_glmqlfit_robust": "FALSE",
    "decoupler_runulm_batch_size": "10000",
    "decoupler_runulm_minn": "5",
    "decoupler_runulm_verbose": "False",
    "decoupler_runulm_useraw": "True"  
}