Package: alevinQC 1.23.1

Charlotte Soneson

alevinQC: Generate QC Reports For Alevin Output

Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications.

Authors:Charlotte Soneson [aut, cre], Avi Srivastava [aut], Rob Patro [aut], Dongze He [aut]

alevinQC_1.23.1.tar.gz
alevinQC_1.23.1.zip(r-4.5)alevinQC_1.23.1.zip(r-4.4)alevinQC_1.23.1.zip(r-4.3)
alevinQC_1.23.1.tgz(r-4.5-x86_64)alevinQC_1.23.1.tgz(r-4.5-arm64)alevinQC_1.23.1.tgz(r-4.4-x86_64)alevinQC_1.23.1.tgz(r-4.4-arm64)alevinQC_1.23.1.tgz(r-4.3-x86_64)alevinQC_1.23.1.tgz(r-4.3-arm64)
alevinQC_1.23.1.tar.gz(r-4.5-noble)alevinQC_1.23.1.tar.gz(r-4.4-noble)
alevinQC_1.23.1.tgz(r-4.4-emscripten)alevinQC_1.23.1.tgz(r-4.3-emscripten)
alevinQC.pdf |alevinQC.html✨
alevinQC/json (API)
NEWS

# Install 'alevinQC' in R:

install.packages('alevinQC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/csoneson/alevinqc/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:alevinQC-1.23.1(bioc 3.21)alevinQC-1.22.0(bioc 3.20)

qualitycontrol singlecell cpp

6.89 score 31 stars 21 scripts 376 downloads 16 exports 82 dependencies

Last updated 2 months agofrom:9ef304b365. Checks:1 OK, 10 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 20 2025
R-4.5-win-x86_64	NOTE	Feb 20 2025
R-4.5-mac-x86_64	NOTE	Feb 20 2025
R-4.5-mac-aarch64	NOTE	Feb 20 2025
R-4.5-linux-x86_64	NOTE	Feb 20 2025
R-4.4-win-x86_64	NOTE	Feb 20 2025
R-4.4-mac-x86_64	NOTE	Feb 20 2025
R-4.4-mac-aarch64	NOTE	Feb 20 2025
R-4.3-win-x86_64	NOTE	Feb 20 2025
R-4.3-mac-x86_64	NOTE	Feb 20 2025
R-4.3-mac-aarch64	NOTE	Feb 20 2025

Exports:alevinFryQCReport alevinFryQCShiny alevinQCReport alevinQCShiny checkAlevinFryInputFiles checkAlevinInputFiles plotAlevinBarcodeCollapse plotAlevinHistogram plotAlevinKneeNbrGenes plotAlevinKneeRaw plotAlevinQuant plotAlevinQuantPairs readAlevinFryQC readAlevinQC simpleafQCReport simpleafQCShiny

Dependencies:base64enc bslib cachem cli colorspace commonmark cowplot cpp11 crayon crosstalk digest dplyr DT evaluate fansi farver fastmap fontawesome forcats fs generics GGally ggplot2 ggstats glue gtable highr hms htmltools htmlwidgets httpuv isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme patchwork pillar pkgconfig plyr prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp rjson rlang rmarkdown sass scales shiny shinydashboard sourcetools stringi stringr tibble tidyr tidyselect tinytex tximport utf8 vctrs viridisLite withr xfun xtable yaml

alevinQC

Charlotte Soneson

Rendered fromalevinqc.Rmdusingknitr::rmarkdownon Feb 20 2025.

Last update: 2024-03-24
Started: 2018-11-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check that all required input files are available for alevin-fry	checkAlevinFryInputFiles
Check that all required input files are available	checkAlevinInputFiles
Summary plot of cell barcode collapsing	plotAlevinBarcodeCollapse
Histogram of selected summary statistic	plotAlevinHistogram
Knee plot of the number of detected genes per cell	plotAlevinKneeNbrGenes
Knee plot of raw cell barcode frequencies	plotAlevinKneeRaw
Panel of plots with quantification summary statistics	plotAlevinQuant
Pairs plot with quantification summary statistics	plotAlevinQuantPairs
Generate alevin/alevin-fry summary report	alevinFryQCReport alevinQCReport qcReport simpleafQCReport
Generate alevin/alevin-fry summary shiny app	alevinFryQCShiny alevinQCShiny qcShiny simpleafQCShiny
Read alevin-fry data required to generate summary report	readAlevinFryQC
Read alevin data required to generate summary report	readAlevinQC