Files in andrewrech/antigen.garnish
Tumor neoantigen prediction
.Rbuildignore
.Rhistory
.dockerignore
.editorconfig
.gitignore
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
NEWS.md
R/antigen.garnish_assemble.R
R/antigen.garnish_io.R
R/antigen.garnish_pkg.R
R/antigen.garnish_predict.R
R/antigen.garnish_run.R
README.md
antigen.garnish.pdf
inst/REFERENCES.bib
inst/extdata/all_alleles.txt
inst/extdata/antigen.garnish_GRCh38_pep.RDS
inst/extdata/antigen.garnish_GRCm38_pep.RDS
inst/extdata/mhcflurry_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/antigen.garnish_transcript_db.R
inst/extdata/src/config_netMHC.sh
inst/extdata/testdata/TUMOR.vcf
inst/extdata/testdata/a.g_ex_netMHCIIpan_af9b5685-733a-49c9.csv
inst/extdata/testdata/a.g_ex_netMHC_906b84c7-7442-4371.csv
inst/extdata/testdata/a.g_ex_netMHCpan_5cf162b8-577c-44ae.csv
inst/extdata/testdata/antigen.garnish_collate_example.txt
inst/extdata/testdata/antigen.garnish_example_affinity_output.txt
inst/extdata/testdata/antigen.garnish_example_frameshifts.txt
inst/extdata/testdata/antigen.garnish_example_input.txt
inst/extdata/testdata/antigen.garnish_example_output.txt
inst/extdata/testdata/antigen.garnish_example_peptide_with_WT_input.txt
inst/extdata/testdata/antigen.garnish_merge_predictions_input_dt.RDS
inst/extdata/testdata/antigen.garnish_netMHC_test_output.RDS
inst/extdata/testdata/antigen.garnish_test.vcf
inst/extdata/testdata/antigen.garnish_test_make_BLAST_uuid.csv
man/antigen.garnish.Rd
man/dissimilarity_score.Rd
man/foreignness_score.Rd
man/garnish_affinity.Rd
man/garnish_antigens.Rd
man/garnish_variants.Rd
man/list_mhc.Rd
tests/manual/test-peptide_window.R
tests/testthat.R
tests/testthat/antigen.garnish_collate_example.txt
tests/testthat/setup.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-dissimilarity_score.R
tests/testthat/test-ex_cDNA.R
tests/testthat/test-garnish_affinity.R
tests/testthat/test-garnish_antigens.R
tests/testthat/test-get_metadata.R
tests/testthat/test-get_pred_commands.R
tests/testthat/test-get_snpeff.R
tests/testthat/test-get_vcf_info_dt.R
tests/testthat/test-get_vcf_sample_dt.R
tests/testthat/test-immune_epitope_database_calculation.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-make_sw_alignment.R
tests/testthat/test-merge_predictions.R
tests/testthat/test-netMHC-download-links.R
tests/testthat/test-paths.R
tests/testthat/test-prediction_output.R
tests/testthat/test-run_netMHC.R
tests/testthat/test-translate_cDNA.R
tests/testthat/test-write_netmhc_nmers.R
