Package: countsimQC 1.25.0

Charlotte Soneson

countsimQC: Compare Characteristic Features of Count Data Sets

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

Authors:Charlotte Soneson [aut, cre]

countsimQC_1.25.0.tar.gz
countsimQC_1.25.0.zip(r-4.5)countsimQC_1.25.0.zip(r-4.4)countsimQC_1.25.0.zip(r-4.3)
countsimQC_1.25.0.tgz(r-4.4-any)countsimQC_1.25.0.tgz(r-4.3-any)
countsimQC_1.25.0.tar.gz(r-4.5-noble)countsimQC_1.25.0.tar.gz(r-4.4-noble)
countsimQC_1.25.0.tgz(r-4.4-emscripten)countsimQC_1.25.0.tgz(r-4.3-emscripten)
countsimQC.pdf |countsimQC.html✨
countsimQC/json (API)
NEWS

# Install 'countsimQC' in R:

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

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

Datasets:

countsimExample - Example list with three count data sets
countsimExample_dfmat - Example list with three count data sets in different formats

On BioConductor:countsimQC-1.25.0(bioc 3.21)countsimQC-1.24.0(bioc 3.20)

microbiome rnaseq singlecell experimentaldesign qualitycontrol reportwriting visualization immunooncology

7.69 score 27 stars 24 scripts 454 downloads 6 mentions 2 exports 122 dependencies

Last updated 14 hours agofrom:cc0eb4d83b. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 22 2024
R-4.5-win	OK	Dec 03 2024
R-4.5-linux	OK	Dec 22 2024
R-4.4-win	OK	Dec 03 2024
R-4.4-mac	OK	Dec 22 2024
R-4.3-win	OK	Dec 03 2024
R-4.3-mac	OK	Dec 22 2024

Exports:countsimQCReport generateIndividualPlots

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob bslib cachem caTools cli codetools colorspace cpp11 crayon crosstalk curl DBI DelayedArray DESeq2 digest dplyr DT edgeR evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png promises purrr R6 ragg randtests rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment survival sys systemfonts textshaping tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XML xtable XVector yaml

countsimQC - Comparing characteristic features across count data sets

Charlotte Soneson

Rendered fromcountsimQC.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2020-04-19
Started: 2017-05-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example list with three count data sets	countsimExample
Example list with three count data sets in different formats	countsimExample_dfmat
countsimQC	countsimQC-pkg
Generate countsimQC report	countsimQCReport
Generate individual plots from countsimQCReport output	generateIndividualPlots