Package: loupeR 1.1.2
Eric Siegel
loupeR: Converts Seurat objects to 10x Genomics Loupe files
Converts Seurat objects to 10x Genomics Loupe files. This is a second line to make the package checker not complain.
Authors:
loupeR_1.1.2.tar.gz
loupeR_1.1.2.zip(r-4.5)loupeR_1.1.2.zip(r-4.4)loupeR_1.1.2.zip(r-4.3)
loupeR_1.1.2.tgz(r-4.4-any)loupeR_1.1.2.tgz(r-4.3-any)
loupeR_1.1.2.tar.gz(r-4.5-noble)loupeR_1.1.2.tar.gz(r-4.4-noble)
loupeR_1.1.2.tgz(r-4.4-emscripten)
loupeR.pdf |loupeR.html✨
loupeR/json (API)
| # Install 'loupeR' in R: |
| install.packages('loupeR', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/10xgenomics/louper/issues
10xgenomicssingle-cell-genomics
Last updated 23 days agofrom:a169417e7a. Checks:OK: 1 NOTE: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 29 2024 |
| R-4.5-win | NOTE | Oct 29 2024 |
| R-4.5-linux | NOTE | Oct 29 2024 |
| R-4.4-win | NOTE | Oct 29 2024 |
| R-4.4-mac | NOTE | Oct 29 2024 |
| R-4.3-win | NOTE | Oct 29 2024 |
| R-4.3-mac | NOTE | Oct 29 2024 |
Exports:counts_matrix_from_assaycreate_bugreportcreate_bugreport_from_seuratcreate_loupecreate_loupe_from_seuratread_feature_ids_from_tsvselect_assayselect_clustersselect_projectionssetupvalidate_barcodesvalidate_clustersvalidate_count_matvalidate_projections
Dependencies:abindaskpassbase64encBHbitbit64bitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolshdf5rherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract the counts matrix from the Assay | counts_matrix_from_assay |
| Create a Bugreport from a count matrix, projections, and clusters | create_bugreport |
| Create a Bugreport from a Seurat Object | create_bugreport_from_seurat |
| Create a Loupe file | create_loupe |
| Create a Loupe file from a Seurat Object | create_loupe_from_seurat |
| Read FeatureIds from 10x features.tsv.gz file | read_feature_ids_from_tsv |
| Select the "best" assay for conversion | select_assay |
| Select clusters from the assay | select_clusters |
| Select projections from the assay | select_projections |
| Setup eula and download executable | setup |
| Validate the format of the barcodes | validate_barcodes |
| Validate the seurat clusters | validate_clusters |
| Validate the seurat count matrix | validate_count_mat |
| Validate the seurat projections | validate_projections |
