Introduction | Data preparation and bioinformatics software | Analysis of 4C-seq data: From aligned reads to near-cis plots | Far-cis and trans interactions | Optional functionality | Session Information
Package: Basic4Cseq 1.49.0
Carolin Walter
Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.
Authors:
Basic4Cseq_1.49.0.tar.gz
Basic4Cseq_1.49.0.zip(r-4.7)Basic4Cseq_1.49.0.zip(r-4.6)Basic4Cseq_1.49.0.zip(r-4.5)
Basic4Cseq_1.49.0.tgz(r-4.6-any)Basic4Cseq_1.49.0.tgz(r-4.5-any)
Basic4Cseq_1.49.0.tar.gz(r-4.7-any)Basic4Cseq_1.49.0.tar.gz(r-4.6-any)
Basic4Cseq_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Basic4Cseq/json (API)
| # Install 'Basic4Cseq' in R: |
| install.packages('Basic4Cseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- liverData - Example 4C-seq data set of fetal liver data
- liverDataRaw - Example 4C-seq data set of fetal liver data
On BioConductor:Basic4Cseq-1.49.0(bioc 3.24)Basic4Cseq-1.48.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyvisualizationqualitycontrolsequencingcoveragealignmentrnaseqsequencematchingdataimport
Last updated from:e0189bb028. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 257 | ||
| linux-devel-x86_64 | OK | 458 | ||
| source / vignettes | OK | 322 | ||
| linux-release-x86_64 | OK | 416 | ||
| macos-release-arm64 | OK | 277 | ||
| macos-oldrel-arm64 | OK | 220 | ||
| windows-devel | OK | 527 | ||
| windows-release | OK | 542 | ||
| windows-oldrel | OK | 530 | ||
| wasm-release | OK | 202 |
Exports:checkRestrictionEnzymeSequencechooseNearCisFragmentscreateVirtualFragmentLibraryData4CseqdrawDigestionFragmentHistogramdrawHeatmapexportVisualizationFragmentDatagetReadDistributiongiveEnzymeSequenceimportVisualizationFragmentDatanearCisFragmentsnearCisFragments<-normalizeFragmentDataplotTransInteractionspointsOfInterestpointsOfInterest<-prepare4CseqDataprintBEDFragmentLibraryprintWigFilerawFragmentsrawFragments<-rawReadsrawReads<-readLengthreadLength<-readPointsOfInterestFilereadsToFragmentssimulateDigestionviewpointChromosomeviewpointChromosome<-viewpointIntervalviewpointInterval<-visualizeViewpoint
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Ecoli.NCBI.20080805caToolscigarillocodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCircosRCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Remove invalid 4C-seq reads from a SAM file | checkRestrictionEnzymeSequence checkRestrictionEnzymeSequence,character,character-method |
| Choose fragments in a provided region around the viewpoint | chooseNearCisFragments chooseNearCisFragments,Data4Cseq,numeric-method |
| Create a virtual fragment library from a provided genome and two restriction enzymes | createVirtualFragmentLibrary createVirtualFragmentLibrary,BSgenome,character,character,numeric-method createVirtualFragmentLibrary,DNAString,character,character,numeric-method |
| Creating a Data4Cseq object | Data4Cseq Data4Cseq,character,numeric,numeric,data.frame,GAlignments-method Data4Cseq,character,numeric,numeric,missing,missing-method |
| Class '"Data4Cseq"' | Data4Cseq-class nearCisFragments nearCisFragments,Data4Cseq-method nearCisFragments<- nearCisFragments<-,Data4Cseq,data.frame-method pointsOfInterest pointsOfInterest,Data4Cseq-method pointsOfInterest<- pointsOfInterest<-,Data4Cseq,data.frame-method rawFragments rawFragments,Data4Cseq-method rawFragments<- rawFragments<-,Data4Cseq,data.frame-method rawReads rawReads,Data4Cseq-method rawReads<- rawReads<-,Data4Cseq,GAlignments-method readLength readLength,Data4Cseq-method readLength<- readLength<-,Data4Cseq,numeric-method viewpointChromosome viewpointChromosome,Data4Cseq-method viewpointChromosome<- viewpointChromosome<-,Data4Cseq,character-method viewpointInterval viewpointInterval,Data4Cseq-method viewpointInterval<- viewpointInterval<-,Data4Cseq,numeric-method |
| Visualize digestion fragments with a histogram | drawDigestionFragmentHistogram drawDigestionFragmentHistogram,data.frame-method |
| Draw a heatmap-like multi-scale contact profile | drawHeatmap drawHeatmap,data.frame-method drawHeatmap,Data4Cseq-method |
| Export near-cis fragment data of a 'Data4Cseq' object | exportVisualizationFragmentData exportVisualizationFragmentData,Data4Cseq,character-method |
| Calculate the read distribution for a 4C-seq experiment | getReadDistribution getReadDistribution,Data4Cseq-method |
| Provide the corresponding enzyme sequence for an enzyme name | giveEnzymeSequence giveEnzymeSequence,character,character-method |
| Import visualization data from a file | importVisualizationFragmentData importVisualizationFragmentData,character-method |
| Example 4C-seq data set of fetal liver data | liverData |
| Example 4C-seq data set of fetal liver data | liverDataRaw |
| Normalize near-cis fragment data read count | normalizeFragmentData normalizeFragmentData,Data4Cseq-method |
| Visualize trans interaction intervals | plotTransInteractions plotTransInteractions,character,character,numeric,character-method plotTransInteractions,data.frame,character,numeric,data.frame-method |
| Alignment and filtering of raw 4C-seq data | prepare4CseqData prepare4CseqData,character,character,character,character-method |
| Print a BED-file fragment library | printBEDFragmentLibrary printBEDFragmentLibrary,character,character-method |
| Print a wig file from 4C-seq read data | printWigFile printWigFile,Data4Cseq-method |
| Read a file with coordinates of marker points | readPointsOfInterestFile readPointsOfInterestFile,character-method |
| Determine fragment coverage of a 4C-seq fragment library | readsToFragments readsToFragments,Data4Cseq,character-method |
| Simulate the digestion of a genome | simulateDigestion simulateDigestion,character,character,BSgenome-method simulateDigestion,character,character,character-method |
| Draw a near-cis coverage plot for 4C-seq data | visualizeViewpoint visualizeViewpoint,data.frame-method visualizeViewpoint,Data4Cseq-method |