Miscellaneous R functions for proteomics analysis. Primarily intended to interface with the R For Mass Spectrometry packages.
library(miniCRAN)
bioc_url <- BiocManager::repositories()[1]
bioc_url## BioCsoft
## "https://bioconductor.org/packages/3.15/bioc"
pkgs <- pkgDep(
"QFeatures",
repos = c(CRAN = "https://cran.r-project.org",
Bioc = bioc_url),
includeBasePkgs = TRUE,
suggests = FALSE
)
sort(pkgs)## [1] "AnnotationFilter" "askpass" "base64enc"
## [4] "Biobase" "BiocGenerics" "bitops"
## [7] "cli" "clue" "cluster"
## [10] "colorspace" "cpp11" "crosstalk"
## [13] "curl" "data.table" "DelayedArray"
## [16] "digest" "dplyr" "ellipsis"
## [19] "fansi" "farver" "fastmap"
## [22] "generics" "GenomeInfoDb" "GenomeInfoDbData"
## [25] "GenomicRanges" "ggplot2" "glue"
## [28] "graphics" "grDevices" "grid"
## [31] "gtable" "htmltools" "htmlwidgets"
## [34] "httr" "igraph" "IRanges"
## [37] "isoband" "jsonlite" "labeling"
## [40] "later" "lattice" "lazyeval"
## [43] "lifecycle" "magrittr" "MASS"
## [46] "Matrix" "MatrixGenerics" "matrixStats"
## [49] "methods" "mgcv" "mime"
## [52] "MsCoreUtils" "MultiAssayExperiment" "munsell"
## [55] "nlme" "openssl" "pillar"
## [58] "pkgconfig" "plotly" "promises"
## [61] "ProtGenerics" "purrr" "QFeatures"
## [64] "R6" "RColorBrewer" "Rcpp"
## [67] "RCurl" "rlang" "S4Vectors"
## [70] "scales" "splines" "stats"
## [73] "stats4" "SummarizedExperiment" "sys"
## [76] "tibble" "tidyr" "tidyselect"
## [79] "tools" "utf8" "utils"
## [82] "vctrs" "viridisLite" "withr"
## [85] "XVector" "yaml" "zlibbioc"