Package: ondisc 1.3.5
Timothy Barry
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 of 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 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_1.3.5.tar.gz
ondisc_1.3.5.tar.gz(r-4.7-arm64)ondisc_1.3.5.tar.gz(r-4.7-x86_64)ondisc_1.3.5.tar.gz(r-4.6-arm64)ondisc_1.3.5.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
ondisc/json (API)
NEWS
| # Install 'ondisc' in R: |
| install.packages('ondisc', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/timothy-barry/ondisc/issues
Pkgdown/docs site:https://timothy-barry.github.io
dataimportsinglecelldifferentialexpressioncrisprcurlopensslcpp
Last updated from:4b32742f90. Checks:5 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 148 | ||
| linux-devel-x86_64 | OK | 159 | ||
| source / vignettes | OK | 229 | ||
| linux-release-arm64 | OK | 201 | ||
| linux-release-x86_64 | OK | 162 | ||
| wasm-release | FAIL | 138 |
Exports:create_odm_from_cellrangercreate_odm_from_r_matrixinitialize_odm_from_backing_filewrite_example_cellranger_dataset
Dependencies:biocmakebitbit64clicliprcpp11crayondata.tabledir.expirydplyrfilelockgenericsgluehmslatticelifecyclemagrittrMatrixpillarpkgconfigprettyunitsprogressR6RcppreadrRhdf5librlangtibbletidyselecttzdbutf8vctrsvroomwithr
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 |
