Introduction | Installation | Input Types | Matrix input | Seurat | SingleCellExperiment | Description of outputs | Results table | Top markers | Options | Dense vs sparse | groups_use
This package is hidden from search results because it is not hosted in the universe of the upstream owner
immunogenomics. To fix this you can add URL: https://satijalab.r-universe.dev/presto to the package DESCRIPTION file. See also theR-universe documentation.Package: presto 1.0.0
Kamil Slowikowski
presto: Fast Functions for Differential Expression using Wilcox and AUC
Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment.
Authors:
presto_1.0.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
presto/json (API)
| # Install 'presto' in R: |
| install.packages('presto', repos = c('https://satijalab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/immunogenomics/presto/issues
Datasets:
- exprs - Small gene expression matrix
- object_sce - SingleCellExperiment object with fake data
- object_seurat - Seurat V3 object with fake data
- y - Group labels for observations in gene expression matrix
Last updated from:a24772a135. Checks:3 WARNING, 2 OK, 8 NOTE. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | WARNING | 243 | ||
| linux-devel-x86_64 | WARNING | 288 | ||
| source / vignettes | OK | 307 | ||
| linux-release-arm64 | NOTE | 237 | ||
| linux-release-x86_64 | NOTE | 260 | ||
| macos-release-arm64 | NOTE | 181 | ||
| macos-release-x86_64 | NOTE | 462 | ||
| macos-oldrel-arm64 | NOTE | 132 | ||
| macos-oldrel-x86_64 | NOTE | 429 | ||
| windows-devel | WARNING | 217 | ||
| windows-release | NOTE | 213 | ||
| windows-oldrel | NOTE | 205 | ||
| wasm-release | OK | 186 |
Exports:%>%collapse_countscompute_hashnnzeroGroupspseudobulk_deseq2pseudobulk_one_vs_allpseudobulk_pairwisepseudobulk_withinrank_matrixsumGroupssummarize_dge_pairstop_markerstop_markers_ddswilcoxauc
Dependencies:clicpp11data.tabledplyrgenericsgluelatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6RcppRcppArmadillorlangstringistringrtibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Collapse counts based on multiple categorical metadata columns | collapse_counts |
| Compute unique hash for each row of data.frame | compute_hash |
| Small gene expression matrix | exprs |
| nnzeroGroups | nnzeroGroups nnzeroGroups.dgCMatrix nnzeroGroups.matrix |
| SingleCellExperiment object with fake data | object_sce |
| Seurat V3 object with fake data | object_seurat |
| Pseudobulk DESeq2 | pseudobulk_deseq2 |
| Pseudobulk one versus all | pseudobulk_one_vs_all |
| Pseudobulk pairwise | pseudobulk_pairwise |
| Pseudobulk within | pseudobulk_within |
| rank_matrix | rank_matrix rank_matrix.dgCMatrix rank_matrix.matrix |
| sumGroups | sumGroups sumGroups.dgCMatrix sumGroups.matrix |
| Summarize differential gene expression pairs | summarize_dge_pairs |
| Get top n markers from wilcoxauc | top_markers |
| Get top n markers from pseudobulk DESeq2 | top_markers_dds |
| Fast Wilcoxon rank sum test and auROC | wilcoxauc wilcoxauc.default wilcoxauc.Seurat wilcoxauc.seurat wilcoxauc.SingleCellExperiment |
| Group labels for observations in gene expression matrix | y |
