Package: RNAseqQC 0.2.1.9000

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_0.2.1.9000.tar.gz
RNAseqQC_0.2.1.9000.zip(r-4.7)RNAseqQC_0.2.1.9000.zip(r-4.6)RNAseqQC_0.2.1.9000.zip(r-4.5)
RNAseqQC_0.2.1.9000.tgz(r-4.6-any)RNAseqQC_0.2.1.9000.tgz(r-4.5-any)
RNAseqQC_0.2.1.9000.tar.gz(r-4.7-any)RNAseqQC_0.2.1.9000.tar.gz(r-4.6-any)
RNAseqQC_0.2.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RNAseqQC/json (API)

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

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:

Conda:

5.83 score 3 stars 113 scripts 391 downloads 20 exports 122 dependencies

Last updated from:d38839a484. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK317
source / vignettesOK320
linux-release-x86_64OK317
macos-release-arm64OK232
macos-oldrel-arm64OK220
windows-develOK312
windows-releaseOK280
windows-oldrelOK260
wasm-releaseOK173

Exports:filter_genesget_gene_idmake_ddsmean_sd_plotplot_biotypesplot_chromosomeplot_geneplot_gene_detectionplot_library_complexityplot_loadingsplot_maplot_pcaplot_pca_scattersplot_sample_boxplotsplot_sample_clusteringplot_sample_ecdfsplot_sample_MAsplot_total_countsplot_within_level_sample_MAssave_plots_to_pdf

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobcachemcigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDESeq2digestdoParalleldplyrensembldbfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggpointdensityggrepelGlobalOptionsgluegtablehttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpatchworkpillarpkgconfigpngProtGenericspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Creating The Example Data Set
Load Packages | Download GSE89888 via recount3 and format data | Differential testing
Rendered fromdata.Rmdusingknitr::rmarkdown

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

RNA-seq Quality Control
Preparations | Input data | Create DESeqDataSet | QC plots on raw count matrix | Total sample counts | Library complexity | Gene detection | Gene biotypes | Gene filtering | Variance stabilization | Chromosomal expression | Replicate variability | Clustering | PCA | Differential expression | Plot a gene | Differential testing | Plot a testing result | SessionInfo
Rendered fromintroduction.Rmdusingknitr::rmarkdown

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