Package: glyenzy 0.6.1


Bin Fu
glyenzy: Deconstruction Glycosylation Biosynthesis
Simulates the biosynthetic process of glycosylation in silico, enabling computational analysis of glycan biosynthesis pathways. Key features include: identifying specific glycosyltransferases responsible for each glycosidic bond at the bond level; reconstructing complete biosynthetic pathways for given glycans; exploring possible transformations between two glycan structures via glycosyltransferases and glycosidases; and predicting glycans that can be synthesized from substrate structures and enzyme sets. The package supports multiple glycan types including N-glycans, O-GalNAc, O-Man, O-GlcNAc, O-Fuc, and O-Glc. As a downstream component of the glycoverse ecosystem, it integrates seamlessly with 'glyrepr', 'glyparse', and 'glymotif' to provide practical, analysis-ready insights into glycan biosynthesis for omics researchers.
Authors:
glyenzy_0.6.1.tar.gz
glyenzy_0.6.1.zip(r-4.7)glyenzy_0.6.1.zip(r-4.6)glyenzy_0.6.1.zip(r-4.5)
glyenzy_0.6.1.tgz(r-4.6-any)glyenzy_0.6.1.tgz(r-4.5-any)
glyenzy_0.6.1.tar.gz(r-4.7-any)glyenzy_0.6.1.tar.gz(r-4.6-any)
glyenzy_0.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
glyenzy/json (API)
| # Install 'glyenzy' in R: |
| install.packages('glyenzy', repos = c('https://glycoverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/glycoverse/glyenzy/issues
Pkgdown/docs site:https://glycoverse.github.io
Last updated from:65ceddfef7 (on v0.6.1). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 744 | ||
| source / vignettes | OK | 231 | ||
| linux-release-x86_64 | OK | 733 | ||
| macos-release-arm64 | OK | 735 | ||
| macos-oldrel-arm64 | OK | 609 | ||
| windows-devel | OK | 1098 | ||
| windows-release | OK | 792 | ||
| windows-oldrel | OK | 777 | ||
| wasm-release | OK | 115 |
Exports:apply_enzymecount_enzymedb_enzymesenzymefind_enzymegrow_glycansgrow_glycans_stephave_enzymemake_enzymematch_enzymepath_biosynthesistrace_biosynthesisview_enzyme
Dependencies:backportscachemcheckmateclicodetoolscpp11digestdplyrfarverfastmapfsfurrrfuturegenericsggplot2globalsglueglydrawglymotifglyparseglyreprgtableigraphisobandlabelinglatticelifecyclelistenvmagrittrMatrixmemoiseparallellypillarpkgconfigpngpurrrR6RColorBrewerrlangrstackdequeS7scalesstringistringrtibbletidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Apply an Enzyme to a Glycan | apply_enzyme |
| Count Enzyme Involvement | count_enzyme |
| Get all enzymes | db_enzymes |
| Enzymes | enzyme |
| Identify Potentially Involved Enzymes | find_enzyme |
| Grow Glycans with Enzymes | grow_glycans grow_glycans_step |
| Determine Whether a Glycan Is Synthesized by a Given Enzyme | have_enzyme |
| Make a Custom Enzyme | make_enzyme |
| Match Residues Added by an Enzyme | match_enzyme |
| Find a Biosynthesis Path Between Glycan Structures | path_biosynthesis |
| Print method for glyenzy_enzyme objects | print.glyenzy_enzyme |
| Trace the Biosynthetic Path of Glycans | trace_biosynthesis |
| View Residues Added by an Enzyme | view_enzyme |