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Package: glyread 0.12.1
Bin Fu
glyread: Read and process glycomics and glycoproteomics data
Provides a unified interface for reading and processing quantification results from various glycomics and glycoproteomics software tools, including Byonic (ByoLogic, pGlycoQuant), StrucGP, pGlyco3 (pGlycoQuant), Glyco-Decipher, GlyHunter, and MSFragger. The package standardizes raw data from different sources, performs peptide-spectrum match (PSM) aggregation, parses glycan compositions and structures, and converts the data into a standardized 'GlycomicSE' and 'GlycoproteomicSE' objects from the 'glyexp' package for downstream analysis within the glycoverse ecosystem.
Authors:
glyread_0.12.1.tar.gz
glyread_0.12.1.zip(r-4.7)glyread_0.12.1.zip(r-4.6)glyread_0.12.1.zip(r-4.5)
glyread_0.12.1.tgz(r-4.6-any)glyread_0.12.1.tgz(r-4.5-any)
glyread_0.12.1.tar.gz(r-4.7-any)glyread_0.12.1.tar.gz(r-4.6-any)
glyread_0.12.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
glyread/json (API)
| # Install 'glyread' in R: |
| install.packages('glyread', repos = c('https://glycoverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/glycoverse/glyread/issues
Pkgdown/docs site:https://glycoverse.github.io
Last updated from:557972b232 (on v0.12.1). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 198 | ||
| source / vignettes | OK | 216 | ||
| linux-release-x86_64 | OK | 218 | ||
| macos-release-arm64 | OK | 161 | ||
| macos-oldrel-arm64 | OK | 135 | ||
| windows-devel | OK | 141 | ||
| windows-release | OK | 152 | ||
| windows-oldrel | OK | 140 | ||
| wasm-release | OK | 135 |
Exports:read_byonic_byologicread_byonic_pglycoquantread_glycan_finderread_glyco_decipherread_glyhunterread_msfraggerread_pglyco3read_pglyco3_pglycoquantread_strucgp
Dependencies:abindAnnotationDbiaskpassbackportsBiobaseBiocBaseUtilsBiocGenericsBiostringsbitbit64blobcachemcellrangercheckmateclicliprcpp11crayoncurlDBIDelayedArraydplyrfastmapfsgenericsGenomicRangesglueglyexpglyparseglyreprhmshttrigraphIRangesjanitorjsonliteKEGGRESTlatticelifecyclelubridatemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6readrreadxlrematchrlangRSQLiterstackdequeS4ArraysS4VectorsSeqinfosnakecaseSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttimechangetzdbutf8vctrsvroomwithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Read Byonic-Byologic result | read_byonic_byologic |
| Read Byonic-pGlycoQuant result | read_byonic_pglycoquant |
| Read GlycanFinder result | read_glycan_finder |
| Read glyco-decipher output | read_glyco_decipher |
| Read GlyHunter result | read_glyhunter |
| Read MSFragger-Glyco result | read_msfragger |
| Read pGlyco3 result | read_pglyco3 |
| Read pGlyco3-pGlycoQuant result | read_pglyco3_pglycoquant |
| Read the result from StrucGP | read_strucgp |