Package: r3Cseq 1.53.0
Supat Thongjuea
r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.
Authors:
r3Cseq_1.53.0.tar.gz
r3Cseq_1.53.0.zip(r-4.5)r3Cseq_1.53.0.zip(r-4.4)r3Cseq_1.53.0.zip(r-4.3)
r3Cseq_1.53.0.tgz(r-4.4-any)r3Cseq_1.53.0.tgz(r-4.3-any)
r3Cseq_1.53.0.tar.gz(r-4.5-noble)r3Cseq_1.53.0.tar.gz(r-4.4-noble)
r3Cseq_1.53.0.tgz(r-4.4-emscripten)r3Cseq_1.53.0.tgz(r-4.3-emscripten)
r3Cseq.pdf |r3Cseq.html✨
r3Cseq/json (API)
NEWS
| # Install 'r3Cseq' in R: |
| install.packages('r3Cseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/supatt-lab/r3cseq/issues
On BioConductor:r3Cseq-1.53.0(bioc 3.21)r3Cseq-1.52.0(bioc 3.20)
Last updated 2 months agofrom:d021c8c642. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:calculateBatchRPMcalculateRPMcontrCoveragecontrInteractionRegionscontrRawDatacontrRawData<-contrReadCountcontrRPMexpCoverageexpInteractionRegionsexport3Cseq2bedGraphexport3CseqRawReads2bedGraphexportBatchInteractions2textexportInteractions2textexpRawDataexpRawData<-expReadCountexpRPMgenerate3CseqReportgetBatchInteractionsgetBatchRawReadsgetBatchReadCountPerRestrictionFragmentgetBatchReadCountPerWindowgetContrInteractionsInRefseqgetCoveragegetExpInteractionsInRefseqgetInteractionsgetRawReadsgetReadCountPerRestrictionFragmentgetReadCountPerWindowgetViewpointplot3CecdfplotDomainogramNearViewpointplotInteractionsNearViewpointplotInteractionsPerChromosomeplotOverviewInteractions
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemchronclicodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegsubfngtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrprotoqvalueR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraysqldfstringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsVGAMviridisLitewithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calculate read per million (RPM) for replicates analysis | calculateBatchRPM calculateBatchRPM,r3CseqInBatch-method |
| calculate read per million (RPM) | calculateRPM calculateRPM,r3Cseq-method |
| This method has been removed. | contrCoverage contrCoverage,r3Cseq-method |
| get interaction regions from the control | contrInteractionRegions contrInteractionRegions,r3CseqCommon-method |
| Accessors for the 'contrRawData' slot of a r3Cseq object. | contrRawData contrRawData,r3Cseq-method contrRawData<- contrRawData<-,r3Cseq-method |
| get read count per region for the control | contrReadCount contrReadCount,r3CseqCommon-method |
| get read per million (RPM) for the control | contrRPM contrRPM,r3CseqCommon-method |
| Rebase The Restriction Enzyme Database | enzymeDb |
| This method has been removed. | expCoverage expCoverage,r3Cseq-method |
| get interaction regions from the experiment | expInteractionRegions expInteractionRegions,r3CseqCommon-method |
| export interaction regions to the 'bedGraph' format | export3Cseq2bedGraph export3Cseq2bedGraph,r3Cseq-method |
| export the interaction signal from the raw reads to the 'bedGraph' format | export3CseqRawReads2bedGraph export3CseqRawReads2bedGraph,r3Cseq-method |
| export identified interaction regions to the tab separated format for replicates analysis | exportBatchInteractions2text exportBatchInteractions2text,r3CseqInBatch-method |
| export identified interaction regions to the tab separated format | exportInteractions2text exportInteractions2text,r3Cseq-method |
| Accessors for the 'expRawData' slot of a r3Cseq object. | expRawData expRawData,r3Cseq-method expRawData<- expRawData<-,r3Cseq-method |
| get read count per region for the experiment | expReadCount expReadCount,r3CseqCommon-method |
| get read per million (RPM) for the experiment | expRPM expRPM,r3CseqCommon-method |
| generate reports for analysis results from r3Cseq | generate3CseqReport generate3CseqReport,r3Cseq-method generate3CseqReport,r3CseqInBatch-method |
| calculate z-score, assign p-value and q-value for each interaction region for replicates data sets | getBatchInteractions getBatchInteractions,r3CseqInBatch-method |
| Get aligned reads from the replicates BAM files | getBatchRawReads getBatchRawReads,r3CseqInBatch-method |
| count reads for replicates analysis | getBatchReadCountPerRestrictionFragment getBatchReadCountPerRestrictionFragment,r3CseqInBatch-method |
| count reads per window size for replicates analysis | getBatchReadCountPerWindow getBatchReadCountPerWindow,r3CseqInBatch-method |
| identified significant interaction regions for RefSeq genes | getContrInteractionsInRefseq getContrInteractionsInRefseq,r3Cseq-method |
| This method has been removed. | getCoverage getCoverage,r3Cseq-method |
| identified significant interaction regions for RefSeq genes | getExpInteractionsInRefseq getExpInteractionsInRefseq,r3Cseq-method |
| calculate z-score, assign p-value and q-value for each interaction region | getInteractions getInteractions,r3Cseq-method |
| Get aligned reads from the BAM file | getRawReads getRawReads,r3Cseq-method |
| count reads per resitrcition fragment | getReadCountPerRestrictionFragment getReadCountPerRestrictionFragment,r3Cseq-method |
| count reads per window size | getReadCountPerWindow getReadCountPerWindow,r3Cseq-method |
| get the viewpoint of 3C-seq data | getViewpoint getViewpoint,r3Cseq-method |
| hg18's refGenes | hg18refGene |
| hg19's refGenes | hg19refGene |
| mm10's refGenes | mm10refGene |
| mm9's refGenes | mm9refGene |
| Myb_prom_FB a data set for the example of r3Cseq analysis | Myb_prom_FB |
| Myb_prom_FL a data set for the example of r3Cseq analysis | Myb_prom_FL |
| This method has been removed. | plot3Cecdf plot3Cecdf,r3Cseq-method |
| Plot domainogram of interaction regions near the viewpoint | plotDomainogramNearViewpoint plotDomainogramNearViewpoint,r3Cseq-method |
| Plot identified interaction regions near the viewpoint | plotInteractionsNearViewpoint plotInteractionsNearViewpoint,r3Cseq-method |
| Plot interaction regions per each chromosome of interest | plotInteractionsPerChromosome plotInteractionsPerChromosome,r3Cseq-method |
| Plot overview of identified interaction regions for genome-wide | plotOverviewInteractions plotOverviewInteractions,r3Cseq-method |
| r3Cseq objects | r3Cseq r3Cseq-class |
| r3CseqCommon objects | r3CseqCommon r3CseqCommon-class |
| r3CseqInBatch objects | r3CseqInBatch r3CseqInBatch-class |
| rn5's refGenes | rn5refGene |