Package: bnbc 1.29.0

Kipper Fletez-Brant

bnbc: Bandwise normalization and batch correction of Hi-C data

Tools to normalize (several) Hi-C data from replicates.

Authors:Kipper Fletez-Brant [cre, aut], Kasper Daniel Hansen [aut]

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bnbc.pdf |bnbc.html✨
bnbc/json (API)
NEWS

# Install 'bnbc' in R:

install.packages('bnbc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hansenlab/bnbc/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

cgEx - Sample chr22 Data

On BioConductor:bnbc-1.29.0(bioc 3.21)bnbc-1.28.0(bioc 3.20)

hic preprocessing normalization software

4.18 score 1 stars 15 scripts 438 downloads 1 mentions 25 exports 133 dependencies

Last updated 23 days agofrom:c54d071716. Checks:ERROR: 2 WARNING: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 01 2024
R-4.5-win-x86_64	WARNING	Nov 01 2024
R-4.5-linux-x86_64	ERROR	Nov 01 2024
R-4.4-win-x86_64	WARNING	Nov 01 2024
R-4.4-mac-x86_64	WARNING	Nov 01 2024
R-4.4-mac-aarch64	WARNING	Nov 01 2024
R-4.3-win-x86_64	WARNING	Nov 01 2024
R-4.3-mac-x86_64	WARNING	Nov 01 2024
R-4.3-mac-aarch64	WARNING	Nov 01 2024

Exports:band band<-bnbc boxSmoother cg2bedgraph2 cgApply cgBandApply colData colData<-ContactGroup contacts contacts<-distanceIdx dropGroupZeros gaussSmoother getBandIdx getBandMatrix getChrCGFromCools getChrIdx getGroupZeros librarySize logCPM rowData rowData<-show

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob bslib cachem cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray digest EBImage edgeR evaluate fansi farver fastmap fftwtools fontawesome formatR fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable HiCBricks highr hms htmltools htmlwidgets httr IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png preprocessCore prettyunits progress R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment survival sva sys tibble tidyselect tiff tinytex tzdb UCSC.utils utf8 vctrs viridis viridisLite vroom withr xfun XML xtable XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bandwise normalization and batch correction of Hi-C data	bnbc-package
Get Band	band band<-
Normalize Contact Matrices with BNBC	bnbc
Apply-type methods	cgApply cgBandApply
Sample chr22 Data	cgEx
Class '"ContactGroup"'	colData,ContactGroup-method colData<-,ContactGroup,DataFrame-method ContactGroup ContactGroup-class contacts contacts<- dim,ContactGroup-method distanceIdx librarySize logCPM rowData,ContactGroup-method rowData<-,ContactGroup-method show,ContactGroup-method [,ContactGroup,ANY,ANY,ANY-method
Methods for manipulating cooler files	cg2bedgraph2 getChrCGFromCools getChrIdx getGenomeIdx
Get Band Indices	getBandIdx
Get Band Matrix	getBandMatrix
Group Zero Operations	dropGroupZeros getGroupZeros
Smoothing Operations	boxSmoother gaussSmoother

Usage by other packages (reverse dependencies)