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Package: loupeR 1.1.5

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:Eric Siegel [aut, cre]

loupeR_1.1.5.tar.gz
loupeR_1.1.5.zip(r-4.7)loupeR_1.1.5.zip(r-4.6)loupeR_1.1.5.zip(r-4.5)
loupeR_1.1.5.tgz(r-4.6-any)loupeR_1.1.5.tgz(r-4.5-any)
loupeR_1.1.5.tar.gz(r-4.7-any)loupeR_1.1.5.tar.gz(r-4.6-any)
loupeR_1.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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

On CRAN:

10xgenomics single-cell-genomics

6.66 score 154 stars 1 packages 124 scripts 15 exports 145 dependencies

Last updated from:b1cba07374. Checks:7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	NOTE	263
source / vignettes	OK	219
linux-release-x86_64	NOTE	235
macos-release-arm64	NOTE	154
macos-oldrel-arm64	NOTE	121
windows-devel	NOTE	233
windows-release	NOTE	228
windows-oldrel	NOTE	196
wasm-release	OK	160

Exports:counts_matrix_from_assay create_bugreport create_bugreport_from_seurat create_hdf5 create_loupe create_loupe_from_seurat read_feature_ids_from_tsv select_assay select_clusters select_projections setup validate_barcodes validate_clusters validate_count_mat validate_projections

Dependencies:abind askpass base64enc BH bit bit64 bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools hdf5r here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S7 sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

Citation

Development and contributors

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 an hdf5 interchange file	create_hdf5
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