Package: ondisc 1.0.0

Timothy Barry

ondisc: Fast, Universal, and Intuitive Computing on Large-Scale Single-Cell Data

Single-cell datasets are growing in size, posing challenges as well as opportunities for biology researchers. 'ondisc' (short for "on-disk single cell") enables users to easily and efficiently analyze large-scale single-cell data. 'ondisc' makes computing on large-scale single-cell data FUN: Fast, Universal, and iNtuitive.

Authors:Timothy Barry [aut, cre], Eugene Katsevich [ths], Kathryn Roeder [ths]

ondisc_1.0.0.tar.gz
ondisc_1.0.0.tar.gz(r-4.5-noble)ondisc_1.0.0.tar.gz(r-4.4-noble)
ondisc.pdf |ondisc.html
ondisc/json (API)

# Install 'ondisc' in R:
install.packages('ondisc', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/timothy-barry/ondisc/issues

Pkgdown:https://katsevich-lab.github.io

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

zlibcpp

3.79 score 62 scripts 220 downloads 11 exports 34 dependencies

Last updated 4 years agofrom:e6e8cf782d. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 27 2024
R-4.5-linux-x86_64OKNov 27 2024

Exports:create_ondisc_matrix_from_mtxget_cell_barcodesget_feature_idsget_feature_namesheadmetadata_ondisc_matrixmultimodal_ondisc_matrixncolnrowondisc_matrixshow

Dependencies:bitbit64clicliprcpp11crayondata.tabledplyrfansigenericsgluehmslatticelifecyclemagrittrMatrixpillarpkgconfigprettyunitsprogressR6Rcppreadrrhdf5rhdf5filtersRhdf5librlangtibbletidyselecttzdbutf8vctrsvroomwithr

Tutorial 1: Using the ondisc_matrix class

Rendered fromtutorial_odm_class.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2021-03-05
Started: 2021-03-05

Tutorial 2: Using metadata_ondisc_matrix and multimodal_ondisc_matrix

Rendered fromtutorial_other_classes.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2021-03-05
Started: 2021-03-05

Readme and manuals

Help Manual

Help pageTopics
Create an 'ondisc_matrix' from a .mtx file.create_ondisc_matrix_from_mtx
Get dimensiondim dim,metadata_ondisc_matrix-method dim,multimodal_ondisc_matrix-method dim,ondisc_matrix-method ncol ncol,multimodal_ondisc_matrix-method nrow nrow,multimodal_ondisc_matrix-method
Pull a submatrix into memory using the '[[' operator.extract-odm [[,metadata_ondisc_matrix,ANY,ANY-method [[,multimodal_ondisc_matrix,ANY,ANY-method [[,ondisc_matrix,ANY,ANY-method [[,ondisc_matrix,ANY,missing-method [[,ondisc_matrix,missing,ANY-method [[,ondisc_matrix,missing,missing-method
Get cell barcodes, feature names, and feature IDsget-names get_cell_barcodes get_cell_barcodes,metadata_ondisc_matrix-method get_cell_barcodes,multimodal_ondisc_matrix-method get_cell_barcodes,ondisc_matrix-method get_feature_ids get_feature_ids,metadata_ondisc_matrix-method get_feature_ids,multimodal_ondisc_matrix-method get_feature_ids,ondisc_matrix-method get_feature_names get_feature_names,metadata_ondisc_matrix-method get_feature_names,multimodal_ondisc_matrix-method get_feature_names,ondisc_matrix-method
headhead,ondisc_matrix-method
'metadata_ondisc_matrix' classmetadata_ondisc_matrix
'multimodal_ondisc_matrix' classmultimodal_ondisc_matrix
ondisc: A package for out-of-memory computing on single-cell dataondisc
'ondisc_matrix' classondisc_matrix
Print basic information to the consoleshow show,metadata_ondisc_matrix-method show,multimodal_ondisc_matrix-method show,ondisc_matrix-method
Subset using the '[' operator.subset-odm [,metadata_ondisc_matrix,ANY,ANY,missing-method [,metadata_ondisc_matrix,ANY,missing,missing-method [,metadata_ondisc_matrix,missing,ANY,missing-method [,metadata_ondisc_matrix,missing,missing,missing-method [,multimodal_ondisc_matrix,ANY,ANY,ANY-method [,multimodal_ondisc_matrix,missing,ANY,missing-method [,multimodal_ondisc_matrix,missing,missing,missing-method [,ondisc_matrix,ANY,ANY,missing-method [,ondisc_matrix,ANY,missing,missing-method [,ondisc_matrix,missing,ANY,missing-method [,ondisc_matrix,missing,missing,missing-method