Package: mosaics 2.45.0
Dongjun Chung
mosaics: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.
Authors:
mosaics_2.45.0.tar.gz
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mosaics_2.45.0.tgz(r-4.4-x86_64)mosaics_2.45.0.tgz(r-4.4-arm64)mosaics_2.45.0.tgz(r-4.3-x86_64)mosaics_2.45.0.tgz(r-4.3-arm64)
mosaics_2.45.0.tar.gz(r-4.5-noble)mosaics_2.45.0.tar.gz(r-4.4-noble)
mosaics_2.45.0.tgz(r-4.4-emscripten)mosaics_2.45.0.tgz(r-4.3-emscripten)
mosaics.pdf |mosaics.html✨
mosaics/json (API)
NEWS
| # Install 'mosaics' in R: |
| install.packages('mosaics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:mosaics-2.43.0(bioc 3.20)mosaics-2.42.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
chipseqsequencingtranscriptiongeneticsbioinformatics
Last updated 17 days agofrom:43771c2f4f. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | OK | Oct 31 2024 |
| R-4.5-linux-x86_64 | OK | Oct 30 2024 |
| R-4.4-win-x86_64 | OK | Oct 31 2024 |
| R-4.4-mac-x86_64 | OK | Oct 31 2024 |
| R-4.4-mac-aarch64 | OK | Oct 31 2024 |
| R-4.3-win-x86_64 | OK | Oct 31 2024 |
| R-4.3-mac-x86_64 | OK | Oct 31 2024 |
| R-4.3-mac-aarch64 | OK | Oct 31 2024 |
Exports:adjustBoundarybdBinchrIDconstructBinsconv_1Sconv_2ScoordempFDRestimatesexportextractReadsfilterPeakfindSummitgcContentgenerateWiginputmappabilitymosaicsFitmosaicsFitHMMmosaicsPeakmosaicsPeakHMMmosaicsRunAllplotpostProbprintreadreadBinsreadCoverageseqDepthshowtagCount
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMASSMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppRhtslibRsamtoolsS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) | mosaics-package mosaics |
| Adjust boundaries of peak regions | adjustBoundary adjustBoundary,MosaicsPeak-method |
| Class "BinData" | BinData-class chrID chrID,BinData-method coord coord,BinData-method gcContent gcContent,BinData-method input input,BinData-method mappability mappability,BinData-method plot,BinData,missing-method print,BinData-method seqDepth seqDepth,BinData-method show,BinData-method tagCount tagCount,BinData-method |
| Construct bin-level ChIP-sep data from an aligned read file | constructBins |
| Extract estimates of the fitted MOSAiCS model | estimates estimates,MosaicsFit-method |
| Export peak calling results to text files | export export,MosaicsPeak-method |
| Load read-level data and extract reads corresponding to each peak region | extractReads extractReads,MosaicsPeak-method |
| Filter out potentially false positive peaks | filterPeak filterPeak,MosaicsPeak-method |
| Find a summit for each peak region | findSummit findSummit,MosaicsPeak-method |
| Construct wiggle files from an aligned ChIP-sep read file | generateWig |
| Fit MOSAiCS model | mosaicsFit mosaicsFit,BinData-method |
| Class "MosaicsFit" | MosaicsFit-class plot,MosaicsFit,ANY-method print,MosaicsFit-method seqDepth,MosaicsFit-method show,MosaicsFit-method |
| Class "MosaicsFitEst" | MosaicsFitEst-class |
| Fit MOSAiCS-HMM model | mosaicsFitHMM mosaicsFitHMM,MosaicsFit-method |
| Class "MosaicsFitParam" | MosaicsFitParam-class |
| Class "MosaicsHMM" | estimates,MosaicsHMM-method MosaicsHMM-class plot,MosaicsHMM,missing-method print,MosaicsHMM-method seqDepth,MosaicsHMM-method show,MosaicsHMM-method |
| Call peaks using fitted MOSAiCS model | mosaicsPeak mosaicsPeak,MosaicsFit-method |
| Class "MosaicsPeak" | bdBin bdBin,MosaicsPeak-method empFDR empFDR,MosaicsPeak-method MosaicsPeak-class plot,MosaicsPeak,missing-method postProb postProb,MosaicsPeak-method print,MosaicsPeak-method read read,MosaicsPeak-method readCoverage readCoverage,MosaicsPeak-method seqDepth,MosaicsPeak-method show,MosaicsPeak-method |
| Call broad peaks using fitted MOSAiCS-HMM model | mosaicsPeakHMM mosaicsPeakHMM,MosaicsHMM-method |
| Class "MosaicsPeakParam" | MosaicsPeakParam-class |
| Analyze ChIP-seq data using the MOSAiCS framework | mosaicsRunAll |
| Import bin-level ChIP-sep data | readBins |
| Class "TagData" | TagData-class |
