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-4.5)scPloidy_0.6.2.zip(r-4.4)scPloidy_0.6.2.zip(r-4.3)
scPloidy_0.6.2.tgz(r-4.4-any)scPloidy_0.6.2.tgz(r-4.3-any)
scPloidy_0.6.2.tar.gz(r-4.5-noble)scPloidy_0.6.2.tar.gz(r-4.4-noble)
scPloidy_0.6.2.tgz(r-4.4-emscripten)scPloidy_0.6.2.tgz(r-4.3-emscripten)
scPloidy.pdf |scPloidy.html✨
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:

SHR_m154211 - Liver Cells from a Rat
SU008_Tumor_Pre_fragmentoverlap - Basal cell carcinoma sample SU008_Tumor_Pre
SU008_Tumor_Pre_windowcovariates - Basal cell carcinoma sample SU008_Tumor_Pre
rescnv - Basal cell carcinoma sample SU008_Tumor_Pre

On CRAN:

5.52 score 3 stars 8 scripts 492 downloads 4 exports 102 dependencies

Last updated 5 months agofrom:d521e8923f. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 31 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 01 2024

Exports:%>%cnv fragmentoverlapcount ploidy

Dependencies:askpass base64enc BH BiocGenerics BiocParallel Biostrings bitops bslib cachem cli coda codetools colorspace cpp11 crayon crosstalk curl data.table digest dplyr evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite kernlab knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime mixtools munsell nimble nlme numDeriv openssl pillar pkgconfig plotly pracma promises purrr R6 rappdirs RColorBrewer Rcpp Rhtslib rlang rmarkdown Rsamtools S4Vectors sass scales segmented snow stringi stringr survival sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

Identify Copy Number Variations (CNVs) in cancer cells

Rendered fromCNV.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Introduction to scPloidy

Rendered fromintro.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Infer Copy Number Variations (CNVs) in Cancer Cells from ATAC-seq Fragment Overlap	cnv
Count Overlap of ATAC-seq Fragments	fragmentoverlapcount
Basal cell carcinoma sample SU008_Tumor_Pre	GSE129785_SU008_Tumor_Pre rescnv SU008_Tumor_Pre_fragmentoverlap SU008_Tumor_Pre_windowcovariates
Infer Ploidy from ATAC-seq Fragment Overlap	ploidy
Liver Cells from a Rat	SHR_m154211