Package: CRMetrics 0.3.2

Rasmus Rydbirk

CRMetrics: Cell Ranger Output Filtering and Metrics Visualization

Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) <doi:10.1038/ncomms14049>. 'CRMetrics' allows for easy plotting of output metrics across multiple samples as well as comparative plots including statistical assessments of these. 'CRMetrics' allows for easy removal of ambient RNA using 'SoupX' by Matthew D Young and Sam Behjati (2020) <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) <https://github.com/kharchenkolab/pagoda2> or 'Seurat' by Yuhan Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) <doi:10.1016/j.cels.2018.11.005> or 'DoubletDetection' by Gayoso et al. (2020) <doi:10.5281/zenodo.2678041>. In the end, cells are filtered based on user input for use in downstream applications.

Authors:Rasmus Rydbirk [aut, cre], Fabienne Kick [aut], Henrietta Holze [aut], Xian Xin [ctb]

CRMetrics_0.3.2.tar.gz
CRMetrics_0.3.2.zip(r-4.5)CRMetrics_0.3.2.zip(r-4.4)CRMetrics_0.3.2.zip(r-4.3)
CRMetrics_0.3.2.tgz(r-4.4-any)CRMetrics_0.3.2.tgz(r-4.3-any)
CRMetrics_0.3.2.tar.gz(r-4.5-noble)CRMetrics_0.3.2.tar.gz(r-4.4-noble)
CRMetrics_0.3.2.tgz(r-4.4-emscripten)CRMetrics_0.3.2.tgz(r-4.3-emscripten)
CRMetrics.pdf |CRMetrics.html
CRMetrics/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/khodosevichlab/crmetrics/issues

On CRAN:

4.18 score 5 stars 7 scripts 260 downloads 3 exports 104 dependencies

Last updated 2 days agofrom:cb44dfc5b4. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winNOTENov 04 2024
R-4.5-linuxNOTENov 04 2024
R-4.4-winNOTENov 04 2024
R-4.4-macNOTENov 04 2024
R-4.3-winNOTENov 04 2024
R-4.3-macERRORNov 04 2024

Exports:CRMetricsread10xread10xH5

Dependencies:abindbackportsbeeswarmBHbootbroomcarcarDataclicodetoolscolorspaceconfintrcorrplotcowplotcpp11DerivdoBydplyrdqrngfansifarverFNNFormulagenericsggbeeswarmggplot2ggpmiscggppggpubrggrepelggsciggsignifgluegridExtragtableigraphirlbaisobandlabelinglatticelifecyclelme4lmodel2lubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrmultcompmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpbmcapplypillarpkgconfigplyrpolynompROCpurrrquantregR6RColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressrlangRSpectrarstatixsandwichscalessccoresitmoSparseMsparseMatrixStatssplus2RstringistringrsurvivalTH.datatibbletidyrtidyselecttimechangeutf8uwotvctrsviporviridisLitewithrxtszoo