Title: Generating Various Numerical Representation Schemes of Protein
Description: Comprehensive toolkit for generating various numerical
representation schemes of protein sequence. The descriptors and similarity
scores included are extensively utilized in bioinformatics and

chemogenomics research. For full functionality, ncbi-blast+ is required.
Suggests: Biostrings, GOSemSim, foreach, doParallel, org.Hs.eg.db

scores included are extensively used in bioinformatics and chemogenomics.
For full functionality, the software 'ncbi-blast+' is needed, see

Author: Nan Xiao <me@nanx.me>, Qingsong Xu <qsxu@csu.edu.cn>,

Title: Generating Various Numerical Representation Schemes for Protein
features of protein sequences described in Xiao et al. (2015)
the software 'ncbi-blast+' is needed, see
person("Dongsheng", "Cao", role = "aut")

person("Dong-Sheng", "Cao", role = "aut")
Suggests: knitr, rmarkdown, Biostrings, GOSemSim, foreach, doParallel,

person("Dong-Sheng", "Cao", role = "aut"))

Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Schopper et al. (2017) <doi:10.1038/nprot.2017.100>) 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.
Imports: rlang, dplyr, stringr, magrittr, data.table, janitor,
progress, purrr, tidyr, ggplot2, forcats, tibble, plotly,
Suggests: testthat, covr, knitr, rmarkdown, proDA, limma, dendextend,
pheatmap, heatmaply, viridis, iq, furrr, future, parallel,
seriation, drc, naniar, httr, igraph, stringi, STRINGdb
Packaged: 2021-04-21 17:16:14 UTC; jan-philippquast

Description: 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.
Packaged: 2021-05-10 08:49:19 UTC; jan-philippquast