Files in ncborcherding/Trex
Methods for TCR single-cell embedding
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pr-commands.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS
R/.Rapp.history
R/CoNGAfy.R
R/Trex.Data.R
R/Trex.database.R
R/annotateDB.R
R/encoder.R
R/geometric.R
R/global.R
R/quietTCRgenes.R
R/runTrex.R
R/trex_example.R
R/utils.R
README.md
_pkgdown.yml
data/Trex.Data.rda
data/Trex.database.rda
data/trex_example.rda
inst/WORDLIST
inst/extdata/TRA_AF_AE.h5
inst/extdata/TRA_AF_VAE.h5
inst/extdata/TRA_KF_AE.h5
inst/extdata/TRA_KF_VAE.h5
inst/extdata/TRA_OHE_AE.h5
inst/extdata/TRA_OHE_VAE.h5
inst/extdata/TRB_AF_AE.h5
inst/extdata/TRB_AF_VAE.h5
inst/extdata/TRB_KF_AE.h5
inst/extdata/TRB_KF_VAE.h5
inst/extdata/TRB_OHE_AE.h5
inst/extdata/TRB_OHE_VAE.h5
man/CoNGAfy.Rd
man/Trex.Data.Rd
man/Trex.database.Rd
man/annotateDB.Rd
man/maTrex.Rd
man/quietTCRgenes.Rd
man/runTrex.Rd
man/trex_example.Rd
tests/spelling.R
tests/testthat.R
tests/testthat/helper-testingFunctions.R
tests/testthat/test-CoNGAfy.R
tests/testthat/test-annotateDB.R
tests/testthat/test-maTrex.R
tests/testthat/test-quietTCRgenes.R
tests/testthat/test-runTrex.R
tests/testthat/testdata/CoNGAfy/CoNGAfy_ADT_counts.rds
tests/testthat/testdata/CoNGAfy/CoNGAfy_counts.rds
tests/testthat/testdata/CoNGAfy/CoNGAfy_mean_counts.rds
tests/testthat/testdata/CoNGAfy/CoNGAfy_mean_meta.data.rds
tests/testthat/testdata/CoNGAfy/CoNGAfy_meta.data.rds
tests/testthat/testdata/annotateDB/annotateDB_TRA_meta.data.rds
tests/testthat/testdata/annotateDB/annotateDB_TRB_meta.data.rds
tests/testthat/testdata/quietTCRgenes/quietTCRgenes_feature.vector.rds
tests/testthat/testdata/runTrex/SCE.object.rds
tests/testthat/testdata/runTrex/maTrex_Geometric.rds
tests/testthat/testdata/runTrex/maTrex_TRA_AE_OHE.rds
tests/testthat/testdata/runTrex/maTrex_TRB_VAE_AF.rds
tests/testthat/testdata/runTrex/runTrex_SCE_TRA_geometric_reduction.rds
tests/testthat/testdata/runTrex/runTrex_TRA_VAE_AF_reduction.rds
tests/testthat/testdata/runTrex/runTrex_TRB_AE_kF_reduction.rds
tests/testthat/testdata/runTrex/runTrex_TRB_VAE_OHE_reduction.rds
tests/testthat/testdata/runTrex/runTrex_TRB_geometric_reduction.rds
vignettes/vignette.Rmd
www/graphicalAbstract.png
www/training_info.png
www/trex_hex.png
