Two Flavors: _col() and _row() | Virtual Index Columns | Complete Function Reference | Core Data Manipulation Functions | Advanced Slicing Functions | Joining Functions | Function-by-Function Examples | Selection | Arrangement | Mutation | Slicing | Renaming | Joining | When dplyr-Style Functions Cannot Help | Why Doesn't glyexp Implement All dplyr Functions? | Common Pitfalls and How to Avoid Them | Pitfall 1: Using glyexp Functions on Non-SE Objects | Pitfall 2: Forgetting the Synchronization | Pitfall 3: Trying to Remove Index Columns | Pitfall 4: Mismatched Operations | Performance Considerations | Philosophy Behind the Design
Package: glyexp 0.16.0
Bin Fu
glyexp: Glycoproteomics and Glycomics Experiments
Provides a tidy data framework for managing glycoproteomics and glycomics experimental data. The 'GlycomicSE' and 'GlycoproteomicSE' classes extend 'SummarizedExperiment' with validated glycomics and glycoproteomics schemas. The package provides dplyr-style data manipulation functions (filter, mutate, select, arrange, slice, join) for seamless data wrangling. As the data core of the 'glycoverse' ecosystem, it provides consistent interfaces for data exchange and analysis workflows.
Authors:
glyexp_0.16.0.tar.gz
glyexp_0.16.0.zip(r-4.7-any)glyexp_0.16.0.zip(r-4.6-any)glyexp_0.16.0.zip(r-4.5-any)
glyexp_0.16.0.tgz(r-4.6-any)glyexp_0.16.0.tgz(r-4.5-any)
glyexp_0.16.0.tar.gz(r-4.7-any)glyexp_0.16.0.tar.gz(r-4.6-any)
glyexp_0.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
glyexp/json (API)
| # Install 'glyexp' in R: |
| install.packages('glyexp', repos = c('https://glycoverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/glycoverse/glyexp/issues
Pkgdown/docs site:https://glycoverse.github.io
Datasets:
- real_experiment - Real glycoproteomics experiment
- real_experiment2 - Real glycomics experiment
Last updated from:4d1f055a5d (on v0.16.0). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 282 | ||
| source / vignettes | OK | 307 | ||
| linux-release | OK | 276 | ||
| macos-release | OK | 182 | ||
| macos-oldrel | OK | 165 | ||
| windows-devel | OK | 218 | ||
| windows-release | OK | 202 | ||
| windows-oldrel | OK | 203 | ||
| wasm-release | OK | 134 |
Exports:.GlycomicSE.GlycoproteomicSEanti_join_colanti_join_obsanti_join_rowanti_join_vararrange_colarrange_obsarrange_rowarrange_varas_glycomic_seas_glycoproteomic_seas_pseudo_glycomeas_seexperimentfilter_colfilter_obsfilter_rowfilter_varfrom_seget_exp_typeget_expr_matget_glycan_typeget_meta_dataget_sample_infoget_var_infoGlycomicSEGlycoproteomicSEinner_join_colinner_join_obsinner_join_rowinner_join_varis_experimentis_glycomic_seis_glycoproteomic_seleft_join_colleft_join_obsleft_join_rowleft_join_varmutate_colmutate_obsmutate_rowmutate_varn_samplesn_variablesrename_colrename_obsrename_rowrename_varsamplesselect_colselect_obsselect_rowselect_varsemi_join_colsemi_join_obssemi_join_rowsemi_join_varset_exp_typeset_glycan_typeset_meta_datashowslice_colslice_head_colslice_head_obsslice_head_rowslice_head_varslice_max_colslice_max_obsslice_max_rowslice_max_varslice_min_colslice_min_obsslice_min_rowslice_min_varslice_obsslice_rowslice_sample_colslice_sample_obsslice_sample_rowslice_sample_varslice_tail_colslice_tail_obsslice_tail_rowslice_tail_varslice_varstandardize_variablesummarize_experimentvariables
Dependencies:abindbackportsBiobaseBiocGenericscheckmateclicpp11DelayedArraydplyrgenericsGenomicRangesglueglyreprigraphIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpurrrR6rlangrstackdequeS4ArraysS4VectorsSeqinfoSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselectutf8vctrswithrXVector
dplyr-Style Functions
Last update: 2026-07-14
Started: 2025-06-18
Get Started with glyexp
For those familiar with SummarizedExperiment | Getting Started with glyexp | The Expression Matrix | Variable Information | Sample Information | Rownames and colnames | Data Manipulation with glyexp | Background and Design Principles | What's Next?
Last update: 2026-07-14
Started: 2025-06-16
Creating Experiments
Required Components | Step 1: Sample Information (Column Data) | Step 2: Variable Information (Row Data) | Step 3: Expression Matrix | Matching Requirements | Step 4: Creating the Experiment
Last update: 2026-07-14
Started: 2025-09-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Arrange sample or variable information | arrange_col arrange_row |
| Coerce to GlycomicSE | as_glycomic_se is_glycomic_se |
| Coerce to GlycoproteomicSE | as_glycoproteomic_se is_glycoproteomic_se |
| Convert a glycoproteomics experiment to a pseudo-glycome experiment | as_pseudo_glycome |
| Filter samples or variables of an experiment | filter_col filter_row |
| Create a GlycomicSE object | GlycomicSE GlycomicSE-class |
| Create a GlycoproteomicSE object | GlycoproteomicSE GlycoproteomicSE-class |
| Join data to sample or variable information | anti_join_col anti_join_row inner_join_col inner_join_row left_join_col left_join_row semi_join_col semi_join_row |
| Mutate sample or variable information | mutate_col mutate_row |
| Real glycoproteomics experiment | real_experiment |
| Real glycomics experiment | real_experiment2 |
| Rename columns in the sample or variable information tibble | rename_col rename_row |
| Select columns of the sample or variable information tibble | select_col select_row |
| Slice sample or variable information | slice_col slice_head_col slice_head_row slice_max_col slice_max_row slice_min_col slice_min_row slice_row slice_sample_col slice_sample_row slice_tail_col slice_tail_row |
| Standardize variable IDs in an experiment | standardize_variable |
| Identification overview | summarize_experiment |