Package: SingleMoleculeFootprinting 2.1.0

Guido Barzaghi

SingleMoleculeFootprinting: Analysis tools for Single Molecule Footprinting (SMF) data

SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.

Authors:Guido Barzaghi [aut, cre], Arnaud Krebs [aut], Mike Smith [ctb]

SingleMoleculeFootprinting_2.1.0.tar.gz
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SingleMoleculeFootprinting_2.1.0.tgz(r-4.4-any)SingleMoleculeFootprinting_1.13.0.tgz(r-4.3-any)
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SingleMoleculeFootprinting_2.1.0.tgz(r-4.4-emscripten)SingleMoleculeFootprinting_1.13.0.tgz(r-4.3-emscripten)
SingleMoleculeFootprinting.pdf |SingleMoleculeFootprinting.html✨
SingleMoleculeFootprinting/json (API)

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

Peer review:

Bug tracker:https://github.com/krebslabrep/singlemoleculefootprinting/issues

On BioConductor:SingleMoleculeFootprinting-2.1.0(bioc 3.21)SingleMoleculeFootprinting-2.0.0(bioc 3.20)

dnamethylationcoveragenucleosomepositioningdatarepresentationepigeneticsmethylseqqualitycontrolsequencing

6.20 score 2 stars 25 scripts 182 downloads 38 exports 174 dependencies

Last updated 25 days agofrom:4352241a0c. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winERROROct 31 2024
R-4.5-linuxERROROct 31 2024
R-4.4-winERROROct 31 2024
R-4.4-macERROROct 31 2024
R-4.3-winERRORSep 28 2024
R-4.3-macERRORSep 28 2024

Exports:Arrange_TFBSs_clustersBaitCaptureBinMethylationCallContextMethylationcbind.fill.MatrixCollapseStrandsCollapseStrandsSMCollectCompositeDataCompositeMethylationCorrelationCompositePlotConversionRateCoverageFilterCreate_MethylationCallingWindowsDetectExperimentTypeFilterByConversionRateFilterContextCytosinesGetQuasRprjGetSingleMolMethMatMaskSNPspanel.corpanel.histpanel.jetPlotAvgSMFPlotSingleMoleculeStackPlotSingleSiteSMFPlotSMrbind.fill.MatrixSingleTFStatesSortReadsSortReadsBySingleTFSortReadsBySingleTF_MultiSiteWrapperSortReadsByTFClusterSortReadsByTFCluster_MultiSiteWrapperStateQuantificationStateQuantificationBySingleTFStateQuantificationByTFPairStateQuantificationPlotTFPairStates

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbroomBSgenomebslibcachemcallrcellrangerclicliprcodetoolscolorspaceconflictedcpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdigestdplyrdtplyrevaluatefansifarverfastmapfilelockfontawesomeforcatsformatRfsfutile.loggerfutile.optionsgarglegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2ggpointdensityggrepelgluegoogledrivegooglesheets4gridExtragtablehavenhighrhmshtmltoolshttrhttr2hwriteridsinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralifecyclelubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemodelrmunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrplyrangespngprettyunitsprocessxprogresspspurrrpwalignQuasRR6raggrappdirsRbowtieRColorBrewerRcppRcppEigenRCurlreadrreadxlrematchrematch2reprexrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4VectorssassscalesselectrShortReadsnowSparseArraystringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytextxdbmakertzdbUCSC.utilsutf8uuidVariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc

FootprintCharter

Rendered fromFootprintCharter.rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-16
Started: 2024-10-10

methylation_calling_and_QCs

Rendered frommethylation_calling_and_QCs.rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-16
Started: 2024-08-12

single_molecule_sorting_by_TF

Rendered fromsingle_molecule_sorting_by_TF.rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-16
Started: 2024-08-12

Readme and manuals

Help Manual

Help pageTopics
Convenience function to arrange a list of given TFBSs into clustersArrange_TFBSs_clusters
Bait capture efficiencyBaitCapture
Summarize methylation inside sorting binsBinMethylation
Call Context MethylationCallContextMethylation
Implementation performing a similar operation of rbind.fill.Matrix but for columnscbind.fill.Matrix
Collapse strandsCollapseStrands
Collapse strands in single molecule matrixCollapseStrandsSM
Collect bulk SMF data for later composite plottingCollectCompositeData
Calculate colMeans after dropping zeroscolMeans_drop0
Composite Methylation RateCompositeMethylationCorrelation
Plot composite SMF dataCompositePlot
Conversion rateConversionRate
Filter Cs for coverageCoverageFilter
Create methylation calling windows to call context methylation in one run for clusters lying proximally to each otherCreate_MethylationCallingWindows
Detect type of experimentDetectExperimentType
Recalculate *_T and *_M values in MethGR object after filtering reads e.g. for conversion ratefilter_reads_from_MethGR
Calculate reads conversion rateFilterByConversionRate
Filter Cytosines in contextFilterContextCytosines
Utility function to perform the dplyr full_join operation on GRanges objectfull.join.granges
Get QuasRprjGetQuasRprj
Get Single Molecule methylation matrixGetSingleMolMethMat
Manipulate GRanges into data.frameGRanges_to_DF
Perform Hierarchical clustering on single readsHierarchicalClustering
Low Coverage Methylation Rate RMSELowCoverageMethRate_RMSE
Utility function to remove cytosines whose MTase target genomic context is affected by SNPsMaskSNPs
Compute MethGR from MethSMMethSM.to.MethGR
Utility for HighCoverage_MethRate_SampleCorrelationpanel.cor
Utility for HighCoverage_MethRate_SampleCorrelationpanel.hist
Utility for HighCoverage_MethRate_SampleCorrelationpanel.jet
Plot low coverage methylation ratePlot_LowCoverageMethRate
Plot Low Coverage Methylation Rate RMSEPlot_LowCoverageMethRate_RMSE
Plot average methylationPlotAvgSMF
Plot single molecule stackPlotSingleMoleculeStack
Plot SMF data at single sitePlotSingleSiteSMF
Wrapper for PlotSingleMoleculeStack functionPlotSM
Implementation performing a similar operation of plyr::rbind.fill.matrix but for sparseMatrixrbind.fill.Matrix
Calculate rowMeans after dropping zerosrowMeans_drop0
Single TF state quantification barSingleTFStateQuantificationPlot
Hard-coded interpretation of biological states from single TF sortingSingleTFStates
Sort reads by single TFSortReads
Wrapper to SortReads for single TF caseSortReadsBySingleTF
Convenience wrapper to sort single molecule according to TFBS clusters at multiple sites in the genomeSortReadsBySingleTF_MultiSiteWrapper
Wrapper to SortReads for TF cluster caseSortReadsByTFCluster
Convenience wrapper to sort single molecule according to TFBS clusters at multiple sites in the genomeSortReadsByTFCluster_MultiSiteWrapper
Convenience for calculating state frequenciesStateQuantification
Convenience for calculating state frequencies after sorting reads by single TFStateQuantificationBySingleTF
Convenience for calculating state frequencies after sorting reads by TF pairStateQuantificationByTFPair
Plot states quantification barStateQuantificationPlot
Subset Granges for given samplesSubsetGRangesForSamples
TF pair state quantification barTFPairStateQuantificationPlot
Design states for TF pair caseTFPairStates