Files in RGLab/ImmuneSignatures2
Pre-Processing for HIPC ImmuneSignatures2 Analysis

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/docker-build.yaml

.gitignore

DESCRIPTION

ImmuneSignatures2.Rproj

NAMESPACE

R/Utils.R R/constructFinalEsets.R R/data.R R/geneExpressionCrossStudyNormalization.R R/geneExpressionPreProcessing.R R/geneExpressionTests.R R/immuneResponseCallGeneration.R R/immuneResponsePreProcessing.R R/immuneResponseTests.R R/qualityControl.R R/sharedMetaData.R R/testFinalEsets.R README.md

data-raw/GeneSets.rda

data-raw/SDY1325_Fig1_Data.csv

data-raw/SDY1370_ELISA.csv

data-raw/SDY1370_Elisa_construction.R

data-raw/SDY1370_subjectIdMap.csv

data-raw/btm_list.rds

data-raw/determineAgeCohortSplit.R data-raw/expectedGeMetaDataColumns.R

data-raw/msigdb.v7.1.symbols.gmt

data-raw/pre-vaccination-datasets.R data-raw/pre-vaccination-genesets.R data-raw/sdy1325_map_metadata.R

data-raw/vaccine_map.csv

data-raw/vaccines.R data-raw/yChromosomeGenes.R

data/ageGroups.rda

data/all_genesets.rda

data/expectedGeMetaDataColumns.rda

data/sdy1325_metadata.rda

data/sdy1370_elisa.rda

data/vaccines.rda

data/yChromGenes.rda

inst/docker/Dockerfile

inst/docker/README.md inst/docker/install.R

inst/docker/renv.lock

inst/manuscript_figures/archive/pre_vaccination_manuscript_figures.Rmd inst/manuscript_figures/archive/prevax_randomForest.Rmd inst/manuscript_figures/archive/temporal_figure_5.Rmd inst/manuscript_figures/archive/temporal_manuscript_figures.Rmd inst/manuscript_figures/data_resource.Rmd

inst/manuscript_figures/img/Figure3a.jpg

inst/manuscript_figures/img/HIPCIOF.png

inst/manuscript_figures/img/SummaryIOF.png

inst/manuscript_figures/img/flowdiagramIOF.png

inst/manuscript_figures/pre_vaccination.Rmd inst/manuscript_figures/quality_control_plots/2020_10_27_extendedOld_mds_byStudy.pdf inst/manuscript_figures/quality_control_plots/2020_10_27_old_mds_byGenderImputed.pdf inst/manuscript_figures/quality_control_plots/2020_10_27_old_mds_byStudy.pdf inst/manuscript_figures/quality_control_plots/2020_10_27_old_pca_byGenderImputed.pdf inst/manuscript_figures/random_forest.Rmd inst/manuscript_figures/supplemental/data_summary.Rmd inst/manuscript_figures/supplemental/pca_plots.Rmd inst/manuscript_figures/supplemental/update_ychrom_qc_fields.Rmd inst/manuscript_figures/temporal.Rmd inst/preprocess/build_esets.R inst/preprocess/create_final_esets.Rmd inst/preprocess/generate_base_eset.Rmd inst/preprocess/pull_esets.Rmd

inst/rstudio/Dockerfile

inst/rstudio/README.md inst/rstudio/install.R inst/supplementary_preprocessing/Figure4paper_Final_Aug.Rmd inst/supplementary_preprocessing/Figure4paper_Final_Aug_edit.Rmd inst/supplementary_preprocessing/HIPC_IOF_age_imputation_distributionFIGURE.Rmd inst/supplementary_preprocessing/IOF_RAPToR_age_imputation_all_functions.Rmd inst/supplementary_preprocessing/IOF_RAPToR_age_imputation_best_functions.Rmd inst/supplementary_preprocessing/RAPToR_age_imputation_notebook.rmd

inst/supplementary_preprocessing/adj_path_vt_colors.rda

RGLab/ImmuneSignatures2 documentation built on Dec. 9, 2022, 10:51 a.m.

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RGLab/ImmuneSignatures2
Pre-Processing for HIPC ImmuneSignatures2 Analysis

Files in RGLab/ImmuneSignatures2
Pre-Processing for HIPC ImmuneSignatures2 Analysis

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RGLab/ImmuneSignatures2 Pre-Processing for HIPC ImmuneSignatures2 Analysis

Files in RGLab/ImmuneSignatures2 Pre-Processing for HIPC ImmuneSignatures2 Analysis

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RGLab/ImmuneSignatures2
Pre-Processing for HIPC ImmuneSignatures2 Analysis

Files in RGLab/ImmuneSignatures2
Pre-Processing for HIPC ImmuneSignatures2 Analysis