- Find species represented with the most AMPs in a constructed AMP database and construct positive datasets : Rmd file 01_amp_training_data_preparations.Rmd
- Test BLAST and classification methods : Rmd file 02_method_evaluation_on_proteomes.Rmd
- Use phylogenetic data to assess performance over a taxonomic scale : Rmd file 03_taxonomic_distance_vs_performance.Rmd
The files required to run the code in these Rmd files can be obtained by clicking here or by using the command:
wget 'https://cloudstor.aarnet.edu.au/plus/s/yXYa5zVk5rrvRpz/download' -O data.tgz
tar -zxvf data.tgz R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggtree_3.0.4 randomcoloR_1.1.0.1 broom_0.7.11 ggtext_0.1.1 pals_1.7
[6] treeio_1.16.2 ape_5.6-1 precrec_0.12.7 patchwork_1.1.1 ampir_1.1.0
[11] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.1.1
[16] tidyr_1.1.4 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-2 ellipsis_0.3.2 class_7.3-19 Peptides_2.4.4
[6] fs_1.5.2 aplot_0.1.2 gridtext_0.1.4 dichromat_2.0-0 rstudioapi_0.13
[11] listenv_0.8.0 prodlim_2019.11.13 fansi_1.0.2 lubridate_1.8.0 xml2_1.3.3
[16] codetools_0.2-18 splines_4.1.2 knitr_1.37 jsonlite_1.7.2 pROC_1.18.0
[21] caret_6.0-90 cluster_2.1.2 dbplyr_2.1.1 mapproj_1.2.8 compiler_4.1.2
[26] httr_1.4.2 backports_1.4.1 assertthat_0.2.1 Matrix_1.3-4 fastmap_1.1.0
[31] lazyeval_0.2.2 cli_3.1.0 htmltools_0.5.2 tools_4.1.2 gtable_0.3.0
[36] glue_1.6.0 reshape2_1.4.4 maps_3.4.0 V8_4.0.0 Rcpp_1.0.8
[41] cellranger_1.1.0 vctrs_0.3.8 nlme_3.1-153 iterators_1.0.13 timeDate_3043.102
[46] gower_0.2.2 xfun_0.30 globals_0.14.0 rvest_1.0.2 lifecycle_1.0.1
[51] future_1.23.0 MASS_7.3-54 scales_1.1.1 ipred_0.9-12 hms_1.1.1
[56] parallel_4.1.2 yaml_2.2.1 curl_4.3.2 ggfun_0.0.4 yulab.utils_0.0.4
[61] rpart_4.1-15 stringi_1.7.6 foreach_1.5.1 tidytree_0.3.7 lava_1.6.10
[66] rlang_0.4.12 pkgconfig_2.0.3 evaluate_0.14 lattice_0.20-45 recipes_0.1.17
[71] tidyselect_1.1.1 parallelly_1.30.0 plyr_1.8.6 magrittr_2.0.1 R6_2.5.1
[76] generics_0.1.1 DBI_1.1.2 pillar_1.6.4 haven_2.4.3 withr_2.4.3
[81] survival_3.2-13 nnet_7.3-16 future.apply_1.8.1 modelr_0.1.8 crayon_1.4.2
[86] utf8_1.2.2 tzdb_0.2.0 rmarkdown_2.13 grid_4.1.2 readxl_1.3.1
[91] data.table_1.14.2 ModelMetrics_1.2.2.2 reprex_2.0.1 digest_0.6.29 gridGraphics_0.5-1
[96] stats4_4.1.2 munsell_0.5.0 ggplotify_0.1.0