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The goal of neopeptides is to calculate and explore property indices of peptides for cancer immunotherapy study.
You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("ShixiangWang/neopeptides")
To use neopeptide, blast
is required.
After installation of blast
, you can set the path with
set_blast_path()
# e.g.
# set_blast_path("/Users/wsx/anaconda3/bin/")
Then install required protein database with
install_database()
calc_iedb_score()
- Calculate IEDB Score for Peptides.calc_dissimilarity()
- Calculate Dissimilarity Value to Reference
Proteome for Peptides.library(neopeptides)
calc_iedb_score(c("MTEYKLVVVGAGDVGKSALTIQLIQNHFVDEYDP", "MTEYKLVVVG"))
#> => Running blastp for homology to IEDB antigens..
#> => Summing IEDB local alignments...
#> => Done.
#> => Removing temporary files...
#> peptide iedb_score
#> 1: MTEYKLVVVGAGDVGKSALTIQLIQNHFVDEYDP 5.038247e-01
#> 2: MTEYKLVVVG 5.895595e-05
#> annotation
#> 1: 18142|polyprotein precursor|NP_041724.2|West Nile virus|11082 DVGVSAL
#> 2: 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus|11103 KLVVLG
calc_dissimilarity(c("MTEYKLVVVGAGDVGKSALTIQLIQNHFVDEYDP", "MTEYKLVVVG"))
#> => Running blastp for homology to self antigens..
#> => Summing local alignments...
#> => Done.
#> => Removing temporary files...
#> peptide dissimilarity
#> 1: MTEYKLVVVGAGDVGKSALTIQLIQNHFVDEYDP 0
#> 2: MTEYKLVVVG 0
Revisiting neoantigen depletion signal in the untreated cancer genome. Shixiang Wang, Xuan Wang, Tao Wu, Zaoke He, Huimin Li, Xiaoqin Sun, Xue-Song Liu bioRxiv 2020.05.11.089540; doi: https://doi.org/10.1101/2020.05.11.089540
MIT © 2019-2020 Shixiang Wang, Xue-Song Liu
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