Package: SingleMoleculeFootprinting 2.1.4

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_2.1.4.tar.gz
SingleMoleculeFootprinting_2.1.4.zip(r-4.5)SingleMoleculeFootprinting_2.1.4.zip(r-4.4)
SingleMoleculeFootprinting_2.1.4.tgz(r-4.4-any)
SingleMoleculeFootprinting_2.1.4.tar.gz(r-4.5-noble)SingleMoleculeFootprinting_2.1.4.tar.gz(r-4.4-noble)
SingleMoleculeFootprinting_2.1.4.tgz(r-4.4-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'))

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

6.43 score 2 stars 27 scripts 224 downloads 42 exports 130 dependencies

Last updated 22 days agofrom:6cf43346a5. Checks:1 OK, 4 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winERRORFeb 17 2025
R-4.5-linuxERRORFeb 17 2025
R-4.4-winERRORFeb 17 2025
R-4.4-macERRORFeb 17 2025

Exports:Arrange_TFBSs_clustersBaitCaptureBinMethylationCallContextMethylationcbind_fill_sparseMatrixCollapseStrandsCollapseStrandsSMCollectCompositeDataCompositeMethylationCorrelationCompositePlotConversionRateCoverageFilterCreate_MethylationCallingWindowsDetectExperimentTypeFilterByConversionRateFilterContextCytosinesFootprintCharterGetQuasRprjGetSingleMolMethMatMaskSNPspanel.corpanel.histpanel.jetPlot_FootprintCharter_SMPlotAvgSMFPlotFootprintsPlotSingleMoleculeStackPlotSingleSiteSMFPlotSMrbind_fill_sparseMatrixRollingMeanSingleTFStatesSortReadsSortReadsBySingleTFSortReadsBySingleTF_MultiSiteWrapperSortReadsByTFClusterSortReadsByTFCluster_MultiSiteWrapperStateQuantificationStateQuantificationBySingleTFStateQuantificationByTFPairStateQuantificationPlotTFPairStates

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemcliclustercodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydeldirdigestdplyrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2ggpointdensityggrepelgluegridExtragtablehmshttrhttr2hwriterinterpIRangesisobandjpegjsonliteKEGGRESTlabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemiscToolsmunsellnlmeopensslparallelDistpatchworkpillarpkgconfigplogrplyrangespngprettyunitsprogresspurrrpwalignQuasRR6rappdirsRbowtieRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrXMLxml2XVectoryaml

FootprintCharter

Rendered fromFootprintCharter.rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2025-02-04
Started: 2024-10-10

methylation_calling_and_QCs

Rendered frommethylation_calling_and_QCs.rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2025-02-14
Started: 2024-08-12

single_molecule_sorting_by_TF

Rendered fromsingle_molecule_sorting_by_TF.rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2025-02-14
Started: 2024-08-12

Readme and manuals

Help Manual

Help pageTopics
Detects TF and nucleosome footprints enriched in a single partition.detect.footprints
Gather equivalent footprints by overlaps (and TF identity) under the same indexAggregateFootprints
Annotate detected TF footprints with user-provided TF motif annotationsAnnotateFootprints
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_sparseMatrix but for columnscbind_fill_sparseMatrix
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
Wrapper to run the function detect.footprint across all clusters computed over a single locusDetectFootprints
Fills empty columnsfill.empty.columns
Recalculate *_T and *_M values in MethGR object after filtering reads e.g. for conversion ratefilter_reads_from_MethGR
Filters dense matrixfilter.dense.matrix
Calculate reads conversion rateFilterByConversionRate
Filter Cytosines in contextFilterContextCytosines
Run FootprintCharterFootprintCharter
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
Computes rolling meanmatrix.sliding.window.average
Turn sparse single molecule matrix to denseMethSM.to.dense
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 single molecule heatmaps of footprint detection resultsPlot_FootprintCharter_SM
Plot low coverage methylation ratePlot_LowCoverageMethRate
Plot Low Coverage Methylation Rate RMSEPlot_LowCoverageMethRate_RMSE
Plot average methylationPlotAvgSMF
Plot bulk SMF separately for each partition alognside footprint detection results.PlotFootprints
Plot single molecule stackPlotSingleMoleculeStack
Plot SMF data at single sitePlotSingleSiteSMF
Wrapper for PlotSingleMoleculeStack functionPlotSM
Implementation performing a similar operation of the plyr function rbind.fill.matrix but for sparseMatrixrbind_fill_sparseMatrix
Compute rolling meanRollingMean
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