Package: ondisc 1.2.0
ondisc: Algorithms and data structures for large single-cell expression matrices
Single-cell datasets are growing in size, posing challenges as well as opportunities for genomics researchers. `ondisc` is an R package that facilitates analysis of large-scale single-cell data out-of-core on a laptop or distributed across tens to hundreds processors on a cluster or cloud. In both of these settings, `ondisc` requires only a few gigabytes of memory, even if the input data are tens of gigabytes in size. `ondisc` mainly is oriented toward single-cell CRISPR screen analysis, but ondisc also can be used for single-cell differential expression and single-cell co-expression analyses. ondisc is powered by several new, efficient algorithms for manipulating and querying large, sparse expression matrices.
Authors:
ondisc_1.2.0.tar.gz
ondisc_1.2.0.zip(r-4.5)ondisc_1.2.0.zip(r-4.4)ondisc_1.2.0.zip(r-4.3)
ondisc_1.2.0.tgz(r-4.4-x86_64)ondisc_1.2.0.tgz(r-4.4-arm64)ondisc_1.2.0.tgz(r-4.3-x86_64)ondisc_1.2.0.tgz(r-4.3-arm64)
ondisc_1.2.0.tar.gz(r-4.5-noble)ondisc_1.2.0.tar.gz(r-4.4-noble)
ondisc.pdf |ondisc.html✨
ondisc/json (API)
NEWS
| # Install 'ondisc' in R: |
| install.packages('ondisc', repos = c('https://timothy-barry.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/timothy-barry/ondisc/issues
dataimportsinglecelldifferentialexpressioncrispr
Last updated 5 months agofrom:1522e1f1e1. Checks:ERROR: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Sep 10 2024 |
| R-4.5-win-x86_64 | ERROR | Sep 10 2024 |
| R-4.5-linux-x86_64 | ERROR | Sep 10 2024 |
| R-4.4-win-x86_64 | ERROR | Sep 10 2024 |
| R-4.4-mac-x86_64 | ERROR | Sep 10 2024 |
| R-4.4-mac-aarch64 | ERROR | Sep 10 2024 |
| R-4.3-win-x86_64 | ERROR | Sep 10 2024 |
| R-4.3-mac-x86_64 | ERROR | Sep 10 2024 |
| R-4.3-mac-aarch64 | ERROR | Sep 10 2024 |
Exports:create_odm_from_cellrangercreate_odm_from_r_matrixinitialize_odm_from_backing_filewrite_example_cellranger_dataset
Dependencies:bitbit64clicliprcpp11crayondata.tabledplyrfansigenericsgluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogressR6RcppreadrRhdf5librlangtibbletidyselecttzdbutf8vctrsvroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ondisc: Algorithms and data structures for large single-cell expression matrices | ondisc-package ondisc |
| Load a row of an 'odm' object into memory | [,odm,ANY,missing,missing-method |
| Create 'odm' object from Cell Ranger | create_odm_from_cellranger |
| Create 'odm' object from R matrix | create_odm_from_r_matrix |
| Return the number of columns and rows of an 'odm' object | dim,odm-method |
| Return the rownames of an 'odm' object | dimnames,odm-method rownames |
| Initialize an 'odm' object | initialize_odm_from_backing_file |
| Write example Cell Ranger dataset | write_example_cellranger_dataset |
