Package: scPloidy 0.6.2

scPloidy: Infer Ploidy of Single Cells

Compute ploidy of single cells (or nuclei) based on single-cell (or single-nucleus) ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data <https://github.com/fumi-github/scPloidy>.

Authors:Fumihiko Takeuchi [aut, cre]

scPloidy_0.6.2.tar.gz
scPloidy_0.6.2.zip(r-4.7-any)scPloidy_0.6.2.zip(r-4.6-any)scPloidy_0.6.2.zip(r-4.5-any)
scPloidy_0.6.2.tgz(r-4.6-any)scPloidy_0.6.2.tgz(r-4.5-any)
scPloidy_0.6.2.tar.gz(r-4.7-any)scPloidy_0.6.2.tar.gz(r-4.6-any)
scPloidy_0.6.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
scPloidy/json (API)

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

Bug tracker:https://github.com/fumi-github/scploidy/issues

Datasets:

On CRAN:

Conda:

4.68 score 4 stars 12 scripts 474 downloads 4 exports 97 dependencies

Last updated from:d521e8923f. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK296
source / vignettesOK305
linux-releaseOK294
macos-releaseOK208
macos-oldrelOK193
windows-develOK246
windows-releaseOK249
windows-oldrelOK246
wasm-releaseOK145

Exports:%>%cnvfragmentoverlapcountploidy

Dependencies:askpassbase64encBHBiocGenericsBiocParallelBiostringsbitopsbslibcachemclicodacodetoolscpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonlitekernlabknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixmatrixStatsmemoisemimemixtoolsnimblenlmenumDerivopensslotelpillarpkgconfigplotlypracmapromisespurrrR6rappdirsRColorBrewerRcppRhtslibrlangrmarkdownRsamtoolsS4VectorsS7sassscalessegmentedSeqinfosnowstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

Introduction to scPloidy
Introduction | Usage | Analyzing sample data | Compute overlaps of DNA fragments | Infer ploidy | Analyzing your own data | Using fragments.tsv.gz generated by 10x Cell Ranger | Using BAM file
Rendered fromintro.Rmdusingknitr::rmarkdown

Last update: 2024-04-26
Started: 2022-08-22

Identify Copy Number Variations (CNVs) in cancer cells
Download from GEO | Prepare windows and peaks | Compute fragmentoverlap from fragments | CNV
Rendered fromCNV.Rmdusingknitr::rmarkdown

Last update: 2024-04-26
Started: 2024-04-26