Package: glycoTraitR 1.1.0
Bingyuan Zhang
glycoTraitR: Compute and analyze the glycan structrual traits from GPSM data
GlycoTraitR is an R package for analyzing glycoproteomics data, particularly glycopeptide-spectrum matches (GPSMs). It supports results generated by the pGlyco3 and Glyco-Decipher search engines. The package parses glycan structures, computes monosaccharide compositions and structural traits, and performs differential analysis of glycan heterogeneity. It constructs trait-by-PSM matrices stored in a SummarizedExperiment object, supports user-defined structural motifs, and provides visualization utilities for interpreting glycan trait changes.
Authors:
glycoTraitR_1.1.0.tar.gz
glycoTraitR_1.1.0.zip(r-4.7)glycoTraitR_1.1.0.zip(r-4.6)glycoTraitR_1.1.0.zip(r-4.5)
glycoTraitR_1.1.0.tgz(r-4.6-any)glycoTraitR_1.1.0.tgz(r-4.5-any)
glycoTraitR_1.1.0.tar.gz(r-4.7-any)glycoTraitR_1.1.0.tar.gz(r-4.6-any)
glycoTraitR_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
glycoTraitR/json (API)
NEWS
| # Install 'glycoTraitR' in R: |
| install.packages('glycoTraitR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/matsui-lab/glycotraitr/issues
- glycanDatabase - Glycan annotation reference database
- meta_toyexample - Toy metadata for glycoTraitR examples
On BioConductor:glycoTraitR-1.1.0(bioc 3.24)glycoTraitR-1.0.0(bioc 3.23)
proteomicsmassspectrometryvisualizationsoftware
Last updated from:7775ec53cd. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 177 | ||
| linux-devel-x86_64 | OK | 305 | ||
| source / vignettes | OK | 270 | ||
| linux-release-x86_64 | OK | 320 | ||
| macos-release-arm64 | OK | 158 | ||
| macos-oldrel-arm64 | OK | 193 | ||
| windows-devel | OK | 244 | ||
| windows-release | OK | 241 | ||
| windows-oldrel | OK | 215 | ||
| wasm-release | OK | 147 |
Exports:analyze_trait_changesbuild_glycan_igraphbuild_trait_secompute_glycan_traitspGlyco3_to_treeplot_glycan_treeplot_trait_distributionread_decipher_gpsmread_pGlyco3_gpsmwurcs_to_tree
Dependencies:abindbackportsBiobaseBiocGenericsbootbroomcarcarDataclicolorspacecowplotcpp11DelayedArrayDerivdoBydplyrfarverforecastFormulafracdiffgenericsGenomicRangesggplot2gluegtableigraphIRangesisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrnlmenloptrnnetnumDerivpbapplypbkrtestpillarpkgconfigpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Differential analysis of glycan traits between experimental groups | analyze_trait_changes |
| Construct an igraph representation of a glycan tree | build_glycan_igraph |
| Build a SummarizedExperiment of glycan trait matrices | build_trait_se |
| Compute glycan traits from a parsed glycan tree | compute_glycan_traits |
| Glycan annotation reference database | glycanDatabase |
| Toy metadata for glycoTraitR examples | meta_toyexample |
| Convert a pGlyco3 glycan string into a glycan tree structure | pGlyco3_to_tree |
| Plot a glycan structure represented as an igraph tree | plot_glycan_tree |
| Plot the distribution of a glycan trait across experimental groups | plot_trait_distribution |
| Combine Glyco-Decipher GPSM results into a long-format table | read_decipher_gpsm |
| Import pGlyco3 GPSM results as a long-format table | read_pGlyco3_gpsm |
| Convert a WURCS string into a glycan tree structure | wurcs_to_tree |
