tidymass.RmdYou can install tidymass from GitLab
if(!require(remotes)){
install.packages("remotes")
}
remotes::install_gitlab("tidymass/tidymass")or GitHub
remotes::install_github("tidymass/tidymass")
tidymass::check_tidymass_version()
tidymass::update_tidymass()
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] grid stats4 stats graphics grDevices utils datasets
#> [8] methods base
#>
#> other attached packages:
#> [1] metid_1.2.24 metpath_1.0.2 ggraph_2.0.5
#> [4] tidygraph_1.2.1 ComplexHeatmap_2.12.1 mixOmics_6.20.0
#> [7] lattice_0.20-45 MASS_7.3-57 massstat_1.0.3
#> [10] tidyr_1.2.0 ggfortify_0.4.14 massqc_1.0.5
#> [13] masscleaner_1.0.6 xcms_3.18.0 MSnbase_2.22.0
#> [16] ProtGenerics_1.28.0 S4Vectors_0.34.0 mzR_2.30.0
#> [19] Rcpp_1.0.8.3 Biobase_2.56.0 BiocGenerics_0.42.0
#> [22] BiocParallel_1.30.3 massprocesser_1.0.5 dplyr_1.0.9
#> [25] ggplot2_3.3.6 magrittr_2.0.3 masstools_1.0.8
#> [28] massdataset_1.0.18 tidymass_1.0.6
#>
#> loaded via a namespace (and not attached):
#> [1] ragg_1.2.2 missForest_1.5
#> [3] knitr_1.39 DelayedArray_0.22.0
#> [5] data.table_1.14.2 rpart_4.1.16
#> [7] KEGGREST_1.36.2 RCurl_1.98-1.7
#> [9] doParallel_1.0.17 generics_0.1.3
#> [11] preprocessCore_1.58.0 RANN_2.6.1
#> [13] proxy_0.4-27 future_1.26.1
#> [15] tzdb_0.3.0 ggsci_2.9
#> [17] SummarizedExperiment_1.26.1 assertthat_0.2.1
#> [19] viridis_0.6.2 xfun_0.31
#> [21] hms_1.1.1 jquerylib_0.1.4
#> [23] evaluate_0.15 DEoptimR_1.0-11
#> [25] fansi_1.0.3 progress_1.2.2
#> [27] readxl_1.4.0 igraph_1.3.2
#> [29] DBI_1.1.3 htmlwidgets_1.5.4
#> [31] MsFeatures_1.4.0 rARPACK_0.11-0
#> [33] purrr_0.3.4 ellipsis_0.3.2
#> [35] RSpectra_0.16-1 backports_1.4.1
#> [37] ggcorrplot_0.1.3 deldir_1.0-6
#> [39] MatrixGenerics_1.8.1 vctrs_0.4.1
#> [41] remotes_2.4.2 withr_2.5.0
#> [43] cachem_1.0.6 ggforce_0.3.3
#> [45] itertools_0.1-3 robustbase_0.95-0
#> [47] checkmate_2.1.0 prettyunits_1.1.1
#> [49] cluster_2.1.3 lazyeval_0.2.2
#> [51] crayon_1.5.1 ellipse_0.4.3
#> [53] pkgconfig_2.0.3 tweenr_1.0.2
#> [55] GenomeInfoDb_1.32.2 nnet_7.3-17
#> [57] rlang_1.0.5 globals_0.15.1
#> [59] lifecycle_1.0.1 affyio_1.66.0
#> [61] extrafontdb_1.0 fastDummies_1.6.3
#> [63] MassSpecWavelet_1.62.0 cellranger_1.1.0
#> [65] randomForest_4.7-1.1 rprojroot_2.0.3
#> [67] polyclip_1.10-0 matrixStats_0.62.0
#> [69] rngtools_1.5.2 Matrix_1.4-1
#> [71] base64enc_0.1-3 GlobalOptions_0.1.2
#> [73] png_0.1-7 viridisLite_0.4.0
#> [75] rjson_0.2.21 bitops_1.0-7
#> [77] Biostrings_2.64.0 doRNG_1.8.2
#> [79] shape_1.4.6 stringr_1.4.1
#> [81] parallelly_1.32.0 robust_0.7-0
#> [83] readr_2.1.2 jpeg_0.1-9
#> [85] gridGraphics_0.5-1 scales_1.2.0
#> [87] memoise_2.0.1 plyr_1.8.7
#> [89] zlibbioc_1.42.0 compiler_4.2.1
#> [91] RColorBrewer_1.1-3 pcaMethods_1.88.0
#> [93] clue_0.3-61 rrcov_1.7-0
#> [95] cli_3.3.0 affy_1.74.0
#> [97] XVector_0.36.0 listenv_0.8.0
#> [99] patchwork_1.1.1 pbapply_1.5-0
#> [101] htmlTable_2.4.0 Formula_1.2-4
#> [103] tidyselect_1.1.2 vsn_3.64.0
#> [105] stringi_1.7.8 textshaping_0.3.6
#> [107] yaml_2.3.5 latticeExtra_0.6-30
#> [109] MALDIquant_1.21 ggrepel_0.9.1
#> [111] sass_0.4.1 tools_4.2.1
#> [113] parallel_4.2.1 circlize_0.4.15
#> [115] rstudioapi_0.14 MsCoreUtils_1.8.0
#> [117] foreach_1.5.2 foreign_0.8-82
#> [119] gridExtra_2.3 farver_2.1.1
#> [121] mzID_1.34.0 digest_0.6.29
#> [123] BiocManager_1.30.18 GenomicRanges_1.48.0
#> [125] ncdf4_1.19 httr_1.4.3
#> [127] colorspace_2.0-3 XML_3.99-0.10
#> [129] fs_1.5.2 IRanges_2.30.0
#> [131] splines_4.2.1 yulab.utils_0.0.5
#> [133] pkgdown_2.0.6 graphlayouts_0.8.0
#> [135] ggplotify_0.1.0 plotly_4.10.0
#> [137] systemfonts_1.0.4 fit.models_0.64
#> [139] jsonlite_1.8.0 Rdisop_1.56.0
#> [141] corpcor_1.6.10 R6_2.5.1
#> [143] Hmisc_4.7-0 pillar_1.7.0
#> [145] htmltools_0.5.2 glue_1.6.2
#> [147] fastmap_1.1.0 class_7.3-20
#> [149] codetools_0.2-18 pcaPP_2.0-1
#> [151] mvtnorm_1.1-3 furrr_0.3.0
#> [153] utf8_1.2.2 bslib_0.3.1
#> [155] tibble_3.1.7 zip_2.2.0
#> [157] openxlsx_4.2.5 Rttf2pt1_1.3.10
#> [159] interp_1.1-2 survival_3.3-1
#> [161] limma_3.52.2 rmarkdown_2.14
#> [163] desc_1.4.1 munsell_0.5.0
#> [165] e1071_1.7-11 GetoptLong_1.0.5
#> [167] GenomeInfoDbData_1.2.8 iterators_1.0.14
#> [169] impute_1.70.0 reshape2_1.4.4
#> [171] gtable_0.3.0 extrafont_0.18