Files in linnykos/eSVD2
eSVD2 for performing the eSVD-DE for cohort-wide differential expression analysis
.RData
.Rbuildignore
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/RcppExports.R
R/compute_pvalue.R
R/compute_test_statistic.R
R/data.R
R/data_loader.R
R/data_management.R
R/esvd_family.R
R/fisher_test.R
R/format_covariates.R
R/generate_data.R
R/generate_null.R
R/initialization.R
R/multtest.R
R/nuisance.R
R/optimization.R
R/optimization_helper.R
R/posterior.R
R/reparameterization.R
R/utils.R
R/zzz.R
README.md
_pkgdown.yml
data/gandal_df.rda
data/housekeeping_df.rda
data/sfari_df.rda
data/velmeshev_gene_df.rda
eSVD2.Rproj
inst/include/.Rapp.history
inst/include/eSVD2.h
man/compute_posterior.Rd
man/compute_posterior.default.Rd
man/compute_posterior.eSVD.Rd
man/compute_pvalue.Rd
man/compute_test_statistic.Rd
man/compute_test_statistic.default.Rd
man/compute_test_statistic.eSVD.Rd
man/data_loader.Rd
man/dot-compute_df.Rd
man/dot-reparameterize.Rd
man/estimate_nuisance.Rd
man/estimate_nuisance.default.Rd
man/estimate_nuisance.eSVD.Rd
man/esvd_family.Rd
man/fisher_test.Rd
man/format_covariates.Rd
man/gandal_df.Rd
man/generate_data.Rd
man/generate_null.Rd
man/housekeeping_df.Rd
man/initialize_esvd.Rd
man/multtest.Rd
man/opt_esvd.Rd
man/opt_esvd.default.Rd
man/opt_esvd.eSVD.Rd
man/opt_x.Rd
man/opt_yz.Rd
man/print.esvd_data_loader.Rd
man/reparameterization_esvd_covariates.Rd
man/sfari_df.Rd
man/velmeshev_gene_df.Rd
oldcode/constrained_newton_lbfgs.R
oldcode/plot_tmp.R
src/RcppExports.cpp
src/constrained_newton.cpp
src/data_loader.cpp
src/data_loader.h
src/distribution.h
src/esvd_family.cpp
src/family.cpp
src/family.h
src/family_bernoulli.cpp
src/family_curved_gaussian.cpp
src/family_exponential.cpp
src/family_gaussian.cpp
src/family_neg_binom.cpp
src/family_neg_binom2.cpp
src/family_poisson.cpp
src/gamma_rate.cpp
src/objective.h
src/optimization.cpp
tests/assets/data_generation.R
tests/assets/identification1.rda
tests/assets/initialize_esvd1.rda
tests/assets/synthetic_data.RData
tests/testthat.R
tests/testthat/test_compute_test_statistic.R
tests/testthat/test_fisher_test.R
tests/testthat/test_gamma_rate.R
tests/testthat/test_generate_data.R
tests/testthat/test_initialization.R
tests/testthat/test_nuisance.R
tests/testthat/test_optimization.R
tests/testthat/test_optimization_helper.R
tests/testthat/test_posterior.R
tests/testthat/test_reparameterization.R
tests/testthat/test_utils.R
vignettes/asd-preprocess.Rmd
vignettes/asd-umap.png
vignettes/asd.Rmd
vignettes/eSVD2.Rmd
vignettes/volcano.png
vignettes/volcano_hk.png
