Package: countsimQC 1.31.0

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_1.31.0.tar.gz
countsimQC_1.31.0.zip(r-4.7)countsimQC_1.31.0.zip(r-4.6)countsimQC_1.31.0.zip(r-4.5)
countsimQC_1.31.0.tgz(r-4.6-any)countsimQC_1.31.0.tgz(r-4.5-any)
countsimQC_1.31.0.tar.gz(r-4.7-any)countsimQC_1.31.0.tar.gz(r-4.6-any)
countsimQC_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
countsimQC/json (API)

# 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-1.31.0(bioc 3.24)countsimQC-1.30.0(bioc 3.23)

microbiome rnaseq singlecell experimentaldesign qualitycontrol reportwriting visualization immunooncology

7.86 score 30 stars 40 scripts 6 mentions 2 exports 115 dependencies

Last updated from:7740a95a08. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	220
linux-devel-x86_64	OK	546
source / vignettes	OK	343
linux-release-x86_64	OK	537
macos-release-arm64	OK	265
macos-oldrel-arm64	OK	270
windows-devel	OK	437
windows-release	OK	357
windows-oldrel	OK	476
wasm-release	OK	207

Exports:countsimQCReport generateIndividualPlots

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob bslib cachem caTools cli codetools cpp11 crayon crosstalk curl DBI DelayedArray DESeq2 digest dplyr DT edgeR evaluate farver fastmap fontawesome formatR fs futile.logger futile.options genefilter generics GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig png promises purrr R6 ragg randtests rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment survival sys systemfonts textshaping tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML xtable XVector yaml

countsimQC - Comparing characteristic features across count data sets

Rendered fromcountsimQC.Rmdusingknitr::rmarkdown

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
Generate countsimQC report	countsimQCReport
Generate individual plots from countsimQCReport output	generateIndividualPlots