Files in andrewrech/antigen.garnish
Ensemble Neoepitope Prediction from DNA Variants in R

.DS_Store
.Rbuildignore
.editorconfig
.github/CODEOWNERS
.gitignore
DESCRIPTION
LICENSE
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/.DS_Store
inst/extdata/Refseq_ids.txt
inst/extdata/all_alleles.txt
inst/extdata/antigen.garnish_GRCh38_pep.RDS
inst/extdata/antigen.garnish_GRCm38_pep.RDS
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
inst/extdata/testdata/antigen.garnish_PureCN_example_output.txt
inst/extdata/testdata/antigen.garnish_example.vcf
inst/extdata/testdata/antigen.garnish_example_affinity_output.txt
inst/extdata/testdata/antigen.garnish_example_input.txt
inst/extdata/testdata/antigen.garnish_example_jaffa_input.csv
inst/extdata/testdata/antigen.garnish_example_jaffa_output.txt
inst/extdata/testdata/antigen.garnish_example_mhcflurry_output_42c5.csv
inst/extdata/testdata/antigen.garnish_example_mhcflurry_output_47f2.csv
inst/extdata/testdata/antigen.garnish_example_mhcnuggets_input_gru_H-2-KB_412b.csv
inst/extdata/testdata/antigen.garnish_example_mhcnuggets_input_gru_HLA-A0201_44b3.csv
inst/extdata/testdata/antigen.garnish_example_mhcnuggets_input_lstm_H-2-KB_4632.csv
inst/extdata/testdata/antigen.garnish_example_mhcnuggets_input_lstm_HLA-A0201_4a93.csv
inst/extdata/testdata/antigen.garnish_example_mhcnuggets_output_gru_HLA-A0201_4033.csv
inst/extdata/testdata/antigen.garnish_example_mhcnuggets_output_lstm_HLA-A0201_4930.csv
inst/extdata/testdata/antigen.garnish_example_netMHCIIpan_af9b5685-733a-49c9.csv
inst/extdata/testdata/antigen.garnish_example_netMHC_906b84c7-7442-4371.csv
inst/extdata/testdata/antigen.garnish_example_netMHCpan_5cf162b8-577c-44ae.csv
inst/extdata/testdata/antigen.garnish_full_example_output.txt
inst/extdata/testdata/antigen.garnish_hg19anno_example.vcf
inst/extdata/testdata/antigen.garnish_jaffa_results.csv
inst/extdata/testdata/antigen.garnish_jaffa_results.fasta
inst/extdata/testdata/antigen.garnish_test.vcf
inst/extdata/testdata/antigen.garnish_test_input.xlsx
inst/extdata/testdata/antigen.garnish_test_make_BLAST_uuid.csv
man/antigen.garnish.Rd man/check_dep_versions.Rd man/check_pred_tools.Rd man/collate_netMHC.Rd man/detect_mhc.Rd man/extract_cDNA.Rd man/garnish_affinity.Rd man/garnish_antigens.Rd man/garnish_clonality.Rd man/garnish_fitness.Rd man/garnish_jaffa.Rd man/garnish_plot.Rd man/garnish_slim.Rd man/garnish_summary.Rd man/garnish_variants.Rd man/get_metadata.Rd man/get_pred_commands.Rd man/get_ss_str.Rd man/get_vcf_info_dt.Rd man/get_vcf_sample_dt.Rd man/get_vcf_snpeff_dt.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_affinity.R tests/testthat/test-garnish_affinity_assemble_generate.R tests/testthat/test-garnish_clonality.R tests/testthat/test-garnish_fitness.R tests/testthat/test-garnish_jaffa.R tests/testthat/test-garnish_plot.R tests/testthat/test-garnish_slim.R tests/testthat/test-garnish_summary.R tests/testthat/test-garnish_targets.R tests/testthat/test-garnish_variants.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-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 wiki/Home.md wiki/Installation.md wiki/Package_schematic.md
andrewrech/antigen.garnish documentation built on Aug. 3, 2018, 7:27 p.m.