Package: r3Cseq 1.59.0

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:Supat Thongjuea, MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, UK <[email protected]>

r3Cseq_1.59.0.tar.gz
r3Cseq_1.59.0.zip(r-4.7)r3Cseq_1.59.0.zip(r-4.6)r3Cseq_1.59.0.zip(r-4.5)
r3Cseq_1.59.0.tgz(r-4.6-any)r3Cseq_1.59.0.tgz(r-4.5-any)
r3Cseq_1.59.0.tar.gz(r-4.7-any)r3Cseq_1.59.0.tar.gz(r-4.6-any)
r3Cseq_1.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
r3Cseq/json (API)

# 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-1.59.0(bioc 3.24)r3Cseq-1.58.0(bioc 3.23)

preprocessing sequencing

5.12 score 3 stars 21 scripts 7 mentions 36 exports 86 dependencies

Last updated from:bc9fecfb48. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	531
linux-devel-x86_64	NOTE	747
source / vignettes	OK	681
linux-release-x86_64	NOTE	665
macos-release-arm64	NOTE	364
macos-oldrel-arm64	NOTE	489
windows-devel	NOTE	519
windows-release	NOTE	514
windows-oldrel	NOTE	532
wasm-release	OK	501

Exports:calculateBatchRPM calculateRPM contrCoverage contrInteractionRegions contrRawData contrRawData<-contrReadCount contrRPM expCoverage expInteractionRegions export3Cseq2bedGraph export3CseqRawReads2bedGraph exportBatchInteractions2text exportInteractions2text expRawData expRawData<-expReadCount expRPM generate3CseqReport getBatchInteractions getBatchRawReads getBatchReadCountPerRestrictionFragment getBatchReadCountPerWindow getContrInteractionsInRefseq getCoverage getExpInteractionsInRefseq getInteractions getRawReads getReadCountPerRestrictionFragment getReadCountPerWindow getViewpoint plot3Cecdf plotDomainogramNearViewpoint plotInteractionsNearViewpoint plotInteractionsPerChromosome plotOverviewInteractions

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem chron cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gsubfn gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plyr proto qvalue R6 RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray sqldf stringi stringr SummarizedExperiment sys vctrs VGAM viridisLite withr XML XVector yaml

r3Cseq

Rendered fromr3Cseq.Rnwusingutils::Sweave

Last update: 2015-01-26
Started: 2013-10-31

Citation

Development and contributors

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