Files in xihaoli/STAARpipeline
STAARpipeline for Analyzing Whole-Genome/Whole-Exome Sequencing Data
.Rbuildignore
.github/workflows/R-CMD-check.yaml
.gitignore
.travis.yml
DESCRIPTION
LICENSE.md
NAMESPACE
R/AI_Individual_Analysis.R
R/Dynamic_Window_SCANG.R
R/Gene_Centric_Coding.R
R/Gene_Centric_Coding_cond.R
R/Gene_Centric_Coding_cond_spa.R
R/Gene_Centric_Noncoding.R
R/Gene_Centric_Noncoding_cond.R
R/Gene_Centric_Noncoding_cond_spa.R
R/Individual_Analysis.R
R/Individual_Analysis_cond.R
R/Individual_Analysis_cond_spa.R
R/LD_pruning.R
R/RcppExports.R
R/Sliding_Window.R
R/Sliding_Window_Multiple.R
R/Sliding_Window_Single.R
R/Sliding_Window_cond.R
R/Sliding_Window_cond_spa.R
R/UTR.R
R/UTR_cond.R
R/UTR_cond_spa.R
R/coding.R
R/coding_incl_ptv.R
R/disruptive_missense.R
R/disruptive_missense_cond.R
R/disruptive_missense_cond_spa.R
R/downstream.R
R/downstream_cond.R
R/downstream_cond_spa.R
R/enhancer_CAGE.R
R/enhancer_CAGE_cond.R
R/enhancer_CAGE_cond_spa.R
R/enhancer_DHS.R
R/enhancer_DHS_cond.R
R/enhancer_DHS_cond_spa.R
R/fit_nullmodel.R
R/genesis2staar_nullmodel.R
R/missense.R
R/missense_cond.R
R/missense_cond_spa.R
R/ncRNA.R
R/ncRNA_cond.R
R/ncRNA_cond_spa.R
R/noncoding.R
R/plof.R
R/plof_cond.R
R/plof_cond_spa.R
R/plof_ds.R
R/plof_ds_cond.R
R/plof_ds_cond_spa.R
R/promoter_CAGE.R
R/promoter_CAGE_cond.R
R/promoter_CAGE_cond_spa.R
R/promoter_DHS.R
R/promoter_DHS_cond.R
R/promoter_DHS_cond_spa.R
R/ptv.R
R/ptv_cond.R
R/ptv_cond_spa.R
R/ptv_ds.R
R/ptv_ds_cond.R
R/ptv_ds_cond_spa.R
R/staar2aistaar_nullmodel.R
R/staar2scang_nullmodel.R
R/synonymous.R
R/synonymous_cond.R
R/synonymous_cond_spa.R
R/sysdata.rda
R/upstream.R
R/upstream_cond.R
R/upstream_cond_spa.R
README.md
STAARpipeline.Rproj
appveyor.yml
docs/STAARpipeline_manual.pdf
docs/STAARpipeline_workflow.jpg
inst/include/STAARpipeline.h
inst/include/STAARpipeline_RcppExports.h
man/Dynamic_Window_SCANG.Rd
man/Gene_Centric_Coding.Rd
man/Gene_Centric_Coding_cond.Rd
man/Gene_Centric_Coding_cond_spa.Rd
man/Gene_Centric_Noncoding.Rd
man/Gene_Centric_Noncoding_cond.Rd
man/Gene_Centric_Noncoding_cond_spa.Rd
man/Individual_Analysis.Rd
man/Individual_Analysis_cond.Rd
man/Individual_Analysis_cond_spa.Rd
man/LD_pruning.Rd
man/Sliding_Window.Rd
man/Sliding_Window_cond.Rd
man/Sliding_Window_cond_spa.Rd
man/fit_nullmodel.Rd
man/genesis2staar_nullmodel.Rd
man/ncRNA.Rd
man/ncRNA_cond.Rd
man/ncRNA_cond_spa.Rd
man/staar2scang_nullmodel.Rd
src/Individual_Score_Test.cpp
src/Individual_Score_Test_SPA.cpp
src/Individual_Score_Test_cond.cpp
src/Individual_Score_Test_cond_multi.cpp
src/Individual_Score_Test_denseGRM.cpp
src/Individual_Score_Test_denseGRM_multi.cpp
src/Individual_Score_Test_multi.cpp
src/Individual_Score_Test_sp.cpp
src/Individual_Score_Test_sp_denseGRM.cpp
src/Individual_Score_Test_sp_denseGRM_multi.cpp
src/Individual_Score_Test_sp_multi.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/matrix_flip_mean.cpp
src/matrix_flip_minor.cpp
