protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data
Analysis Tools
Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Version:
0.9.1
Depends:
R (≥ 4.0)
Imports:
rlang,
dplyr,
stringr,
magrittr,
data.table,
janitor,
progress,
purrr,
tidyr,
ggplot2,
forcats,
tibble,
plotly,
ggrepel, utils, grDevices,
curl,
readr,
lifecycle,
httr, methods,
R.utils, stats
Suggests:
testthat,
covr,
knitr,
rmarkdown,
shiny,
r3dmol,
proDA,
limma,
dendextend,
pheatmap,
heatmaply,
furrr,
future, parallel,
seriation,
drc,
igraph,
stringi,
STRINGdb,
iq,
scales,
farver,
ggforce,
xml2,
jsonlite
Published:
2024年10月21日
Author:
Jan-Philipp Quast
ORCID iD
[aut, cre],
Dina Schuster
ORCID iD
[aut],
ETH Zurich [cph, fnd]
Maintainer:
Jan-Philipp Quast <quast at imsb.biol.ethz.ch>
NeedsCompilation:
no
Documentation:
Downloads:
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