Package: BioQC 1.41.0

Jitao David Zhang

BioQC: Detect tissue heterogeneity in expression profiles with gene sets

BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.

Authors:Jitao David Zhang [cre, aut], Laura Badi [aut], Gregor Sturm [aut], Roland Ambs [aut], Iakov Davydov [aut]

BioQC_1.41.0.tar.gz
BioQC_1.41.0.zip(r-4.7-x86_64)BioQC_1.41.0.zip(r-4.7-arm64)BioQC_1.41.0.zip(r-4.6-x86_64)BioQC_1.41.0.zip(r-4.6-arm64)BioQC_1.41.0.zip(r-4.5-x86_64)
BioQC_1.41.0.tgz(r-4.6-x86_64)BioQC_1.41.0.tgz(r-4.6-arm64)BioQC_1.41.0.tgz(r-4.5-x86_64)BioQC_1.41.0.tgz(r-4.5-arm64)
BioQC_1.41.0.tar.gz(r-4.7-arm64)BioQC_1.41.0.tar.gz(r-4.7-x86_64)BioQC_1.41.0.tar.gz(r-4.6-arm64)BioQC_1.41.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BioQC/json (API)

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

Bug tracker:https://github.com/accio/bioqc/issues

Pkgdown/docs site:https://accio.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:BioQC-1.41.0(bioc 3.24)BioQC-1.40.0(bioc 3.23)

geneexpressionqualitycontrolstatisticalmethodgenesetenrichmentcpp

7.70 score 5 stars 1 packages 1 scripts 625 downloads 7 mentions 45 exports 9 dependencies

Last updated from:7aa53c346c. Checks:1 ERROR, 13 NOTE, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR216
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linux-devel-x86_64NOTE253
source / vignettesOK325
linux-release-arm64NOTE172
linux-release-x86_64NOTE243
macos-release-arm64NOTE179
macos-release-x86_64NOTE304
macos-oldrel-arm64NOTE118
macos-oldrel-x86_64NOTE277
windows-devel-arm64NOTE259
windows-devel-x86_64NOTE443
windows-release-arm64NOTE270
windows-release-x86_64NOTE361
windows-oldrel-x86_64NOTE238
wasm-releaseFAIL152

Exports:absLog10pappendGmtListas.GmtListentropyentropyDiversityentropySpecificityfilterBySizefilterPmatgetLeadingEdgeIndexFromMatrixgetLeadingEdgeIndexFromVectorginiGmtListgmtlist2signedGenesetsgsDescgsGeneCountgsGenesgsNamegsNamespacegsNamespace<-gsSizehasNamespaceIndexListisValidBaseIndexListisValidGmtListisValidIndexListisValidSignedGenesetsisValidSignedIndexListmatchGenesoffsetoffset<-prettySigNamesreadCurrentSignaturesreadGmtreadSignedGmtsampleSpecializationsetDescAsNamespacesetNamespaceshowSignedGenesetsSignedIndexListsimplifyMatrixuniqGenesetsByNamespacewmwLeadingEdgewmwTestwmwTestInR

Dependencies:BiobaseBiocGenericsedgeRgenericslatticelimmalocfitRcppstatmod

BioQC Algorithm: Speeding up the Wilcoxon-Mann-Whitney Test
Algorithmic improvements | Time benchmark | Conclusion | R Session Info
Rendered frombioqc-efficiency.Rmdusingknitr::rmarkdown

Last update: 2020-12-06
Started: 2016-11-08

BioQC-benchmark: Testing Efficiency, Sensitivity and Specificity of BioQC on simulated and real-world data
Experiment setup | Sensitivity Benchmark | Mixing Benchmark | Dataset selection and quality control | An example of weighted mixing: heart and jejunum | Pairwise Mixing | Conclusions | Appendix | Comparing BioQC with Principal Component Analysis (PCA) | R Session Info
Rendered frombioqc-simulation.Rmdusingknitr::rmarkdown

Last update: 2020-12-06
Started: 2020-12-06

BioQC-kidney: The kidney expression example
Introduction | Importing the data | Running BioQC | Validation with quantitative RT-PCR | Impact of sample removal on differential gene expression analysis | R Session Info
Rendered fromBioQC.Rmdusingknitr::rmarkdown

Last update: 2020-12-06
Started: 2020-12-06

BioQC: Detect tissue heterogeneity in gene expression data
Introduction | A dummy example | Using basic data structures | Case study with real dataset | Benchmarking against R implementation | Technical notes | Background matters | Acknowledgement | R Session Info
Rendered frombioqc-introduction.Rmdusingknitr::rmarkdown

Last update: 2020-12-06
Started: 2020-12-06

Comparing the Wilcoxon-Mann-Whitney to alternative statistical tests
Computational Performance | R Session Info | References
Rendered frombioqc-wmw-test-performance.Rmdusingknitr::rmarkdown

Last update: 2020-12-06
Started: 2020-12-06

Using BioQC with signed genesets
Introduction | GMT read-in | Expression object construction | Match genes | Perform the analysis | Conclusions | Acknowledgement | R session info
Rendered frombioqc-signedGenesets.Rmdusingknitr::rmarkdown

Last update: 2017-08-02
Started: 2016-08-29

Readme and manuals

Help Manual

Help pageTopics
Subsetting GmtList object into another GmtList object[.GmtList
Subsetting GmtList object to fetch one gene-set[[.GmtList
Absolute base-10 logarithm of p-valuesabsLog10p
Append a GmtList object to another oneappendGmtList
Convert a list of gene symbols into a gmtlistas.GmtList
An S4 class to hold a list of indices, with the possibility to specify the offset of the indices. IndexList and SignedIndexList extend this classBaseIndexList-class
Shannon entropyentropy
Entropy-based sample diversityentropyDiversity
Entropy-based gene-expression specificityentropySpecificity
Filter a GmtList by sizefilterBySize
Filter rows of p-value matrix under the significance thresholdfilterPmat
Getting leading-edge indices from a vectorgetLeadingEdgeIndexFromMatrix getLeadingEdgeIndexFromVector
Calculate Gini Index of a numeric vectorgini
Convert a list to a GmtList objectGmtList
An S4 class to hold geneset in the GMT file in a list, each item in the list is in in turn a list containing following items: name, desc, and genes.GmtList-class
Convert gmtlist into a list of signed genesetsgmtlist2signedGenesets
Gene-set descriptionsgsDesc
Gene-set gene countsgsGeneCount gsSize
Gene-set member genesgsGenes
Gene-set namesgsName
Gene-set namespacesgsNamespace
gsNamespace<- is the synonym of setGsNamespacegsNamespace<-
Whether namespace is sethasNamespace
Convert a list to an IndexList objectIndexList IndexList,list-method IndexList,logical-method IndexList,numeric-method
An S4 class to hold a list of integers as indices, with the possibility to specify the offset of the indicesIndexList-class
Function to validate a BaseIndexList objectisValidBaseIndexList
Function to validate a GmtList objectisValidGmtList
Function to validate an IndexList objectisValidIndexList
Function to validate a SignedGenesets objectisValidSignedGenesets
Function to validate a SignedIndexList objectisValidSignedIndexList
Match genes in a list-like object to a vector of genesymbolsmatchGenes matchGenes,character,character-method matchGenes,character,DGEList-method matchGenes,character,eSet-method matchGenes,character,matrix-method matchGenes,GmtList,character-method matchGenes,GmtList,DGEList-method matchGenes,GmtList,eSet-method matchGenes,GmtList,matrix-method matchGenes,SignedGenesets,character-method matchGenes,SignedGenesets,DGEList-method matchGenes,SignedGenesets,eSet-method matchGenes,SignedGenesets,matrix-method
Get offset from an IndexList objectoffset offset,BaseIndexList-method
Set the offset of an 'IndexList' or a 'SignedIndexList' objectoffset-set offset<- offset<-,IndexList,numeric-method offset<-,SignedIndexList,numeric-method
Prettify default signature namesprettySigNames
Load current BioQC signaturesreadCurrentSignatures
Read in gene-sets from a GMT filereadGmt
Read signed GMT filesreadSignedGmt
Entropy-based sample specializationsampleSpecialization
Set gene-set description as namespacesetDescAsNamespace
Set the namespace field in each gene-set within a GmtListsetNamespace
Show method for GmtListshow,GmtList-method
Show method for IndexListshow,IndexList-method
Show method for SignedGenesetsshow,SignedGenesets-method
Show method for SignedIndexListshow,SignedIndexList-method
Convert a list to a SignedGenesets objectSignedGenesets
An S4 class to hold signed genesets, each item in the list is in in turn a list containing following items: name, pos, and neg.SignedGenesets-class
Convert a list into a SignedIndexListSignedIndexList SignedIndexList,list-method
An S4 class to hold a list of signed integers as indices, with the possibility to specify the offset of the indicesSignedIndexList-class
Simplify matrix in case of single row/columnssimplifyMatrix
Make names of gene-sets unique by namespace, and member genes of gene-sets uniqueuniqGenesetsByNamespace
prints the options of valTypes of wmwTestvalTypes
Identify BioQC leading-edge genes of one gene-setwmwLeadingEdge
Wilcoxon-Mann-Whitney rank sum test for high-throughput expression profiling datawmwTest wmwTest,ANY,list-method wmwTest,ANY,logical-method wmwTest,ANY,numeric-method wmwTest,eSet,GmtList-method wmwTest,eSet,list-method wmwTest,eSet,logical-method wmwTest,eSet,numeric-method wmwTest,eSet,SignedGenesets-method wmwTest,eSet,SignedIndexList-method wmwTest,matrix,GmtList-method wmwTest,matrix,IndexList-method wmwTest,matrix,SignedGenesets-method wmwTest,matrix,SignedIndexList-method wmwTest,numeric,IndexList-method wmwTest,numeric,SignedIndexList-method
Wilcoxon-Mann-Whitney test in RwmwTestInR