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Commit 0a0aee46 authored by Konrad Zych's avatar Konrad Zych
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Revert "updating R version dependency"

This reverts commit cba138e4
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......@@ -10,7 +10,7 @@ build:
stage: build
script:
- R CMD build ./ --no-build-vignettes
- R CMD INSTALL SIAMCAT_0.99.3.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
- mv SIAMCAT_* ./Rscript_flavor
- cd Rscript_flavor
- wget http://congo.embl.de/downloads/siamcat_test_data.tar.gz
......@@ -24,7 +24,7 @@ preprocess_data:
stage: preprocess_data
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.3.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
script:
- Rscript 01_validate_data.r --metadata_in num_metadata_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --metadata_out valMetaData.tsv --label_in label_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --label_out valLabel.tsv --feat_in feat_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --feat_out valFeat.tsv
- Rscript 02_select_samples.r --metadata_in valMetaData.tsv --metadata_out valMetaData_sel.tsv --label_in valLabel.tsv --label_out valLabel_sel.tsv --feat_in valFeat.tsv --feat_out valFeat_sel.tsv --filter_var="age" --allowed_range="[0,120]"
......@@ -47,7 +47,7 @@ train_model:
stage: train_model
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.3.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
script:
- Rscript 09_train_models.r --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --data_split dataSplit.Rdata --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2"
......@@ -64,7 +64,7 @@ make_predictions:
stage: make_predictions
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.3.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
script:
- Rscript 10_make_predictions.r --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --data_split dataSplit.Rdata --pred pred.tsv --mlr_models_list models.RData
......@@ -81,7 +81,7 @@ evaluate_interpret:
stage: evaluate_interpret
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.3.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
script:
- Rscript 11_evaluate_predictions.r --label_in valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
- Rscript 12_interpret_model.r --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --metadata_in valMetaData_sel.tsv --mlr_models_list models.RData --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
......
Package: SIAMCAT
Type: Package
Title: Statistical Inference of Associations between Microbial Communities And host phenoTypes
Version: 0.99.3
Version: 0.99.1
Author: Georg Zeller [aut,cre], Jakob Wirbel[aut], Konrad Zych [aut], Nicolai Karcher[ctb] and Kersten Breuer[ctb]
Authors@R: c(person("Georg", "Zeller", role = c("aut", "cre"), email = "zeller@embl.de", comment = c(ORCID = "0000-0003-1429-7485")),
person("Konrad", "Zych", role = c("aut", "cre"), email = "konrad.zych@embl.de", comment = c(ORCID = "0000-0001-7426-0516")),
......@@ -10,7 +10,7 @@ Authors@R: c(person("Georg", "Zeller", role = c("aut", "cre"), email = "zeller@e
Maintainer: Konrad Zych <konrad.zych@embl.de>, Georg Zeller <eller@embl.de>, Jakob Wirbel <jakob.wirbel@embl.de>
Description: Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).
Depends:
R (>= 3.5.0),
R (>= 3.4.0),
mlr,
phyloseq
Imports:
......
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