Package: scShardSplitRef 0.1.0

scShardSplitRef: Reference Genome Splitting for Single-Cell Multiome Data

Splits chromosomes of large-genome species into smaller shards that respect the maximum contig size supported by 10x Genomics' 'Cell Ranger ARC' reference builder, avoiding breaks inside gene bodies, and rewrites the corresponding 'GTF' annotation coordinates to match. This enables researchers to build custom 'Cell Ranger ARC' references for Multiome 'ATAC' and Gene Expression data from genomes that would otherwise exceed the tool's chromosome size limits.

Authors:Irina Kuznetsova [aut, cre], Luke Pembleton [aut], Luca Curci [aut], Adam H. Sparks [aut], Curtin University [fnd, cph], Grains Research and Development Corporation [fnd, cph]

scShardSplitRef_0.1.0.tar.gz
scShardSplitRef_0.1.0.zip(r-4.7-any)scShardSplitRef_0.1.0.zip(r-4.6-any)scShardSplitRef_0.1.0.zip(r-4.5-any)
scShardSplitRef_0.1.0.tgz(r-4.6-any)scShardSplitRef_0.1.0.tgz(r-4.5-any)
scShardSplitRef_0.1.0.tar.gz(r-4.7-any)scShardSplitRef_0.1.0.tar.gz(r-4.6-any)
scShardSplitRef_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scShardSplitRef/json (API)

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

Bug tracker:https://github.com/irinavkuznetsova/scshardsplitref/issues

On CRAN:

Conda:

5.60 score 2 scripts 177 downloads 3 exports 4 dependencies

Last updated from:d7f40d82ec. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK114
source / vignettesOK171
linux-releaseOK127
macos-releaseOK131
macos-oldrelOK158
windows-develOK79
windows-releaseOK76
windows-oldrelOK73
wasm-releaseOK106

Exports:determine_split_regionsprocess_gtfscShardSplitRef_options

Dependencies:clirlangstringiwithr

scShardSplitRef: Getting Started
Package Overview | Guided Walk-Through | Installation | Prerequisites | Input Files | Step-by-Step Guide | Step-1 | The Help Page for the determine_split_regions() Function | Check formatting of input files and build BED-like split intervals | Step-2 | The Help Page for the process_gtf() Function | Generate Gene Annotation (GTF) File in Compatible to Cell Ranger ARC Format | Step-3 | Step-4 | Prepare config File | Run Cell Ranger ARC | Citation | License | Contributing | Acknowledgements
Rendered fromscShardSplitRef.Rmdusingknitr::rmarkdown

Last update: 2026-07-14
Started: 2026-07-06

scShardSplitRef: Algorithm Description
1. Purpose | 2. {scShardSplitRef} Guided Walkthrough Using a Toy Example | Installation | Prerequisites | Input Files | Workflow | 1. Determine Split Regions | The Help Page for determine_split_regions() | Usage Example: determine_split_regions() | Algorithm Explanation: How determine_split_regions() works | No Overlap with Gene Coordinates | Overlap with Gene Coordinates | 2. Process a GTF file by assigning split-region sequence names | The Help Page for process_gtf() | Usage Example: process_gtf() | 3. Acknowledgements
Rendered fromscShardSplitRefDetailedAlgorithm.Rmdusingknitr::rmarkdown

Last update: 2026-07-13
Started: 2026-06-08