Package: RNAseqQC 0.2.1

RNAseqQC: Quality Control for RNA-Seq Data

Functions for semi-automated quality control of bulk RNA-seq data.

Authors:Frederik Ziebell [cre], Frederik Ziebell [aut], GlaxoSmithKline Research & Development Limited [cph]

RNAseqQC_0.2.1.tar.gz
RNAseqQC_0.2.1.zip(r-4.5)RNAseqQC_0.2.1.zip(r-4.4)RNAseqQC_0.2.1.zip(r-4.3)
RNAseqQC_0.2.1.tgz(r-4.4-any)RNAseqQC_0.2.1.tgz(r-4.3-any)
RNAseqQC_0.2.1.tar.gz(r-4.5-noble)RNAseqQC_0.2.1.tar.gz(r-4.4-noble)
RNAseqQC_0.2.1.tgz(r-4.4-emscripten)RNAseqQC_0.2.1.tgz(r-4.3-emscripten)
RNAseqQC.pdf |RNAseqQC.html
RNAseqQC/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/frederikziebell/rnaseqqc/issues

Datasets:
  • T47D - The T47D cell line data of RNA-seq experiment GSE89888
  • T47D_diff_testing - Differential expression results corresponding to the T47D data set.

On CRAN:

5.18 score 2 stars 25 scripts 403 downloads 18 exports 124 dependencies

Last updated 4 months agofrom:de030dd850. Checks:OK: 6 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxWARNINGNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKOct 13 2024

Exports:filter_genesget_gene_idmake_ddsmean_sd_plotplot_biotypesplot_chromosomeplot_geneplot_gene_detectionplot_library_complexityplot_loadingsplot_maplot_pcaplot_pca_scattersplot_sample_clusteringplot_sample_MAsplot_total_countsplot_within_level_sample_MAssave_plots_to_pdf

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDESeq2digestdoParalleldplyrensembldbfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggpointdensityggrepelGlobalOptionsgluegtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrpngProtGenericspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

Creating The Example Data Set

Rendered fromdata.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-06-21
Started: 2024-06-21

RNA-seq Quality Control

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-06-21
Started: 2024-06-21