Package: qsea 1.33.0
Matthias Lienhard
qsea: IP-seq data analysis and vizualization
qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.
Authors:
qsea_1.33.0.tar.gz
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qsea.pdf |qsea.html✨
qsea/json (API)
NEWS
| # Install 'qsea' in R: |
| install.packages('qsea', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:qsea-1.33.0(bioc 3.21)qsea-1.32.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingdnamethylationcpgislandchipseqpreprocessingnormalizationqualitycontrolvisualizationcopynumbervariationchiponchipdifferentialmethylation
Last updated 2 months agofrom:c55425a96a. Checks:OK: 4 WARNING: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 30 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 30 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 30 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 30 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 30 2024 |
| R-4.3-win-x86_64 | OK | Nov 30 2024 |
| R-4.3-mac-x86_64 | OK | Nov 30 2024 |
| R-4.3-mac-aarch64 | OK | Nov 30 2024 |
Exports:addCNVaddContrastaddCoverageaddEnrichmentParametersaddLibraryFactorsaddNewSamplesaddOffsetaddPatternDensityaddSeqPrefcreateQseaSetfitNBglmgetChrNamesgetCNVgetCountsgetExampleQseaSetgetLibSizegetOffsetgetParametersgetPCAgetRegionsgetSampleGroupsgetSampleNamesgetSampleTablegetWindowSizegetZygosityhasCNVisSignificantmakeTablenormMethodplotCNVplotCoverageplotEnrichmentProfileplotEPmatrixplotPCAplotPCAfactorsregionStatssetZygosity
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecodetoolscpp11crayoncurldata.tableDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgtoolsHMMcopyhttrIRangesjsonlitelambda.rlatticelimmaMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraystatmodSummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| QSEA: Quantitative sequencing enrichment analysis and visualization | qsea-package QSEA qsea |
| estimate CNV information and add to qseaSet object | addCNV |
| fit GLMs to reduced model and test for significance | addContrast |
| Import sequencing data | addCoverage |
| Enrichment analysis | addEnrichmentParameters |
| Estimate effective library size | addLibraryFactors |
| Extends an exisiting qseaSet by new samples | addNewSamples |
| Estimate background reads | addOffset |
| Infer sequence pattern density values and add to qseaSet object | addPatternDensity |
| Add sequence preference to qseaSet object | addSeqPref |
| Prepares a qseaSet Object | createQseaSet |
| Fit GLM for each window | fitNBglm |
| Simulation of MeDIP seq QSEA set | getExampleQseaSet |
| Principle Component Analysis (PCA) in QSea | getPCA |
| Finds Significant Regions | isSignificant |
| Create a Results Table | makeTable |
| Definition of normalization procedure | normMethod |
| Plots a Heatmap-like Overview of the CNVs | plotCNV |
| Plots a genome-browser-like image of a region | plotCoverage |
| Plotting functions for enrichment profiles | plotEnrichmentProfile plotEPmatrix |
| Plots for Principle Component Analysis (PCA) in QSEA | plotPCA plotPCA,qseaPCA-method plotPCAfactors plotPCAfactors,qseaPCA-method |
| qseaGLM class and its methods | addParameters,qseaGLM-method getParameters,qseaGLM-method getSampleNames,qseaGLM-method qseaGLM qseaGLM-class show,qseaGLM-method |
| qseaPCA class and its methods | getSampleNames,qseaPCA-method qseaPCA qseaPCA-class show,qseaPCA-method |
| qseaSet class and its methods | addParameters,qseaSet-method getChrNames getChrNames,qseaSet-method getCNV getCNV,qseaSet-method getCounts getCounts,qseaSet-method getLibSize getLibSize,qseaSet-method getNormFactors getNormFactors,qseaSet-method getOffset getOffset,qseaSet-method getParameters getParameters,qseaSet-method getRegions getRegions,qseaSet-method getSampleGroups getSampleGroups,qseaSet-method getSampleNames getSampleNames,qseaSet-method getSampleTable getSampleTable,qseaSet-method getWindowSize getWindowSize,qseaSet-method getZygosity getZygosity,qseaSet-method hasCNV hasCNV,qseaSet-method qseaSet qseaSet-class setZygosity setZygosity,qseaSet-method show,qseaSet-method |
| Counts the Windows in Regions of Interest | regionStats |