├── .Rhistory ├── Add_QC_label.R ├── Association_Analysis_PreStep.r ├── FAVORannotator_csv ├── Annotate.R ├── Annotation_name_catalog.csv ├── FAVORdatabase_chrsplit.csv ├── Varinfo_gds.R └── gds2agds.R ├── LICENSE.md ├── README.md ├── STAARpipelineSummary_Dynamic_Window.r ├── STAARpipelineSummary_Gene_Centric_Coding.r ├── STAARpipelineSummary_Gene_Centric_Coding_Annotation.r ├── STAARpipelineSummary_Gene_Centric_Noncoding.r ├── STAARpipelineSummary_Gene_Centric_Noncoding_Annotation.r ├── STAARpipelineSummary_Genetic_Region_Annotation.r ├── STAARpipelineSummary_Individual_Analysis.r ├── STAARpipelineSummary_Individual_Analysis_Annotation.r ├── STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning.r ├── STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning_Combination.r ├── STAARpipelineSummary_Known_Loci_Info.r ├── STAARpipelineSummary_Known_Loci_Pruning.r ├── STAARpipelineSummary_Known_Loci_Pruning_Combination.r ├── STAARpipelineSummary_Sliding_Window.r ├── STAARpipeline_Dynamic_Window.r ├── STAARpipeline_Gene_Centric_Coding.r ├── STAARpipeline_Gene_Centric_Coding_Long_Masks.r ├── STAARpipeline_Gene_Centric_Noncoding.r ├── STAARpipeline_Gene_Centric_Noncoding_Long_Masks.r ├── STAARpipeline_Gene_Centric_ncRNA.r ├── STAARpipeline_Gene_Centric_ncRNA_Long_Masks.r ├── STAARpipeline_Individual_Analysis.r ├── STAARpipeline_Null_Model.r ├── STAARpipeline_Null_Model_GENESIS.r ├── STAARpipeline_Null_Model_Multi.r ├── STAARpipeline_STAAR2SCANG.r ├── STAARpipeline_Sliding_Window.r ├── STAARpipeline_processVariantFiles.R ├── batch jobs ├── Annotate.sh ├── STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning.sh ├── STAARpipelineSummary_Known_Loci_Pruning.sh ├── STAARpipeline_Dynamic_Window.sh ├── STAARpipeline_Gene_Centric_Coding.sh ├── STAARpipeline_Gene_Centric_Coding_Long_Masks.sh ├── STAARpipeline_Gene_Centric_Noncoding.sh ├── STAARpipeline_Gene_Centric_Noncoding_Long_Masks.sh ├── STAARpipeline_Gene_Centric_ncRNA.sh ├── STAARpipeline_Individual_Analysis.sh ├── STAARpipeline_Sliding_Window.sh ├── Varinfo_gds.sh └── gds2agds.sh ├── convertVCF2GDS.R └── processVariantFiles.R /.Rhistory: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Add_QC_label.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/Add_QC_label.R -------------------------------------------------------------------------------- /Association_Analysis_PreStep.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/Association_Analysis_PreStep.r -------------------------------------------------------------------------------- /FAVORannotator_csv/Annotate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/FAVORannotator_csv/Annotate.R -------------------------------------------------------------------------------- /FAVORannotator_csv/Annotation_name_catalog.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/FAVORannotator_csv/Annotation_name_catalog.csv -------------------------------------------------------------------------------- /FAVORannotator_csv/FAVORdatabase_chrsplit.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/FAVORannotator_csv/FAVORdatabase_chrsplit.csv -------------------------------------------------------------------------------- /FAVORannotator_csv/Varinfo_gds.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/FAVORannotator_csv/Varinfo_gds.R -------------------------------------------------------------------------------- /FAVORannotator_csv/gds2agds.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/FAVORannotator_csv/gds2agds.R -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/README.md -------------------------------------------------------------------------------- /STAARpipelineSummary_Dynamic_Window.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Dynamic_Window.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Gene_Centric_Coding.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Gene_Centric_Coding.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Gene_Centric_Coding_Annotation.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Gene_Centric_Coding_Annotation.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Gene_Centric_Noncoding.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Gene_Centric_Noncoding.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Gene_Centric_Noncoding_Annotation.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Gene_Centric_Noncoding_Annotation.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Genetic_Region_Annotation.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Genetic_Region_Annotation.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Individual_Analysis.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Individual_Analysis.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Individual_Analysis_Annotation.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Individual_Analysis_Annotation.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning_Combination.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning_Combination.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Known_Loci_Info.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Known_Loci_Info.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Known_Loci_Pruning.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Known_Loci_Pruning.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Known_Loci_Pruning_Combination.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Known_Loci_Pruning_Combination.r -------------------------------------------------------------------------------- /STAARpipelineSummary_Sliding_Window.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipelineSummary_Sliding_Window.r -------------------------------------------------------------------------------- /STAARpipeline_Dynamic_Window.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Dynamic_Window.r -------------------------------------------------------------------------------- /STAARpipeline_Gene_Centric_Coding.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Gene_Centric_Coding.r -------------------------------------------------------------------------------- /STAARpipeline_Gene_Centric_Coding_Long_Masks.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Gene_Centric_Coding_Long_Masks.r -------------------------------------------------------------------------------- /STAARpipeline_Gene_Centric_Noncoding.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Gene_Centric_Noncoding.r -------------------------------------------------------------------------------- /STAARpipeline_Gene_Centric_Noncoding_Long_Masks.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Gene_Centric_Noncoding_Long_Masks.r -------------------------------------------------------------------------------- /STAARpipeline_Gene_Centric_ncRNA.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Gene_Centric_ncRNA.r -------------------------------------------------------------------------------- /STAARpipeline_Gene_Centric_ncRNA_Long_Masks.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Gene_Centric_ncRNA_Long_Masks.r -------------------------------------------------------------------------------- /STAARpipeline_Individual_Analysis.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Individual_Analysis.r -------------------------------------------------------------------------------- /STAARpipeline_Null_Model.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Null_Model.r -------------------------------------------------------------------------------- /STAARpipeline_Null_Model_GENESIS.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Null_Model_GENESIS.r -------------------------------------------------------------------------------- /STAARpipeline_Null_Model_Multi.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Null_Model_Multi.r -------------------------------------------------------------------------------- /STAARpipeline_STAAR2SCANG.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_STAAR2SCANG.r -------------------------------------------------------------------------------- /STAARpipeline_Sliding_Window.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_Sliding_Window.r -------------------------------------------------------------------------------- /STAARpipeline_processVariantFiles.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/STAARpipeline_processVariantFiles.R -------------------------------------------------------------------------------- /batch jobs/Annotate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/Annotate.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipelineSummary_Known_Loci_Individual_Analysis_Pruning.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipelineSummary_Known_Loci_Pruning.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipelineSummary_Known_Loci_Pruning.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipeline_Dynamic_Window.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipeline_Dynamic_Window.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipeline_Gene_Centric_Coding.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipeline_Gene_Centric_Coding.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipeline_Gene_Centric_Coding_Long_Masks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipeline_Gene_Centric_Coding_Long_Masks.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipeline_Gene_Centric_Noncoding.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipeline_Gene_Centric_Noncoding.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipeline_Gene_Centric_Noncoding_Long_Masks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipeline_Gene_Centric_Noncoding_Long_Masks.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipeline_Gene_Centric_ncRNA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipeline_Gene_Centric_ncRNA.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipeline_Individual_Analysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipeline_Individual_Analysis.sh -------------------------------------------------------------------------------- /batch jobs/STAARpipeline_Sliding_Window.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/STAARpipeline_Sliding_Window.sh -------------------------------------------------------------------------------- /batch jobs/Varinfo_gds.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/Varinfo_gds.sh -------------------------------------------------------------------------------- /batch jobs/gds2agds.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/batch jobs/gds2agds.sh -------------------------------------------------------------------------------- /convertVCF2GDS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/convertVCF2GDS.R -------------------------------------------------------------------------------- /processVariantFiles.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xihaoli/STAARpipeline-Tutorial/HEAD/processVariantFiles.R --------------------------------------------------------------------------------