Files in andrewrech/antigen.garnish
Ensemble neoepitope prediction from DNA variants in R

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.gitattributes
.github/CODEOWNERS
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md R/antigen.garnish_assemble.R R/antigen.garnish_fitness.R R/antigen.garnish_io.R R/antigen.garnish_jaffa.R R/antigen.garnish_pkg.R R/antigen.garnish_predict.R R/antigen.garnish_run.R README.md
inst/.DS_Store
inst/REFERENCES.bib
inst/extdata/all_alleles.txt
inst/extdata/install.sh
inst/extdata/mhcflurry_alleles.txt
inst/extdata/mhcnuggets_gru_alleles.txt
inst/extdata/mhcnuggets_lstm_alleles.txt
inst/extdata/netMHCII_alleles.txt
inst/extdata/netMHCIIpan_alleles.txt
inst/extdata/netMHC_alleles.txt
inst/extdata/netMHCpan_alleles.txt
inst/extdata/src/Aligner.py
inst/extdata/src/Aligner.pyc
inst/extdata/src/Neoantigen.py
inst/extdata/src/Neoantigen.pyc
inst/extdata/src/main.py
man/antigen.garnish.Rd man/check_pred_tools.Rd man/collate_netMHC.Rd man/detect_mhc.Rd man/extract_cDNA.Rd man/garnish_fitness.Rd man/garnish_jaffa.Rd man/garnish_plot.Rd man/garnish_predictions.Rd man/garnish_summary.Rd man/garnish_variants.Rd man/get_metadata.Rd man/get_pred_commands.Rd man/get_snpeff.Rd man/get_ss_str.Rd man/list_mhc.Rd man/make_BLAST_uuid.Rd man/make_DAI_uuid.Rd man/make_cDNA.Rd man/make_nmers.Rd man/merge_predictions.Rd man/run_mhcflurry.Rd man/run_mhcnuggets.Rd man/run_netMHC.Rd man/translate_cDNA.Rd man/write_mhcnuggets_nmers.Rd man/write_netmhc_nmers.Rd tests/manual/test-peptide_window.R tests/testthat.R tests/testthat/helper.R tests/testthat/teardown.R tests/testthat/test-cDNA_edge_cases.R tests/testthat/test-collate_netMHC.R tests/testthat/test-detect_mhc.R tests/testthat/test-ex_cDNA.R tests/testthat/test-garnish_fitness.R tests/testthat/test-garnish_jaffa.R tests/testthat/test-garnish_plot.R tests/testthat/test-garnish_predictions.R tests/testthat/test-garnish_predictions_assemble_generate.R tests/testthat/test-garnish_summary.R tests/testthat/test-garnish_variants.R tests/testthat/test-garnish_variants_intersection.R tests/testthat/test-get_metadata.R tests/testthat/test-get_pred_commands.R tests/testthat/test-get_snpeff.R tests/testthat/test-list_mhc.R tests/testthat/test-make_BLAST_uuid.R tests/testthat/test-make_DAI_uuid.R tests/testthat/test-make_cDNA.R tests/testthat/test-make_nmers.R tests/testthat/test-merge_predictions.R tests/testthat/test-prediction_output.R tests/testthat/test-run_mhcnuggets.R tests/testthat/test-run_netMHC.R tests/testthat/test-translate_cDNA.R tests/testthat/test-write_mhcnuggets_nmers.R tests/testthat/test-write_netmhc_nmers.R tests/testthat/test-write_nuggets_nmers.R
andrewrech/antigen.garnish documentation built on Jan. 5, 2018, 6:59 a.m.