Package: HiCParser 1.5.1

Maigné Élise

HiCParser: Parser for HiC data in R

This package is a parser to import HiC data into R. It accepts several type of data: tabular files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files. The HiC data can be several files, for several replicates and conditions. The data is formated in an InteractionSet object.

Authors:Zytnicki Matthias [aut], Maigné Élise [aut, cre]

HiCParser_1.5.1.tar.gz
HiCParser_1.5.1.zip(r-4.7-x86_64)HiCParser_1.5.1.zip(r-4.7-arm64)HiCParser_1.5.1.zip(r-4.6-x86_64)HiCParser_1.5.1.zip(r-4.6-arm64)HiCParser_1.5.1.zip(r-4.5-x86_64)
HiCParser_1.5.1.tgz(r-4.6-x86_64)HiCParser_1.5.1.tgz(r-4.6-arm64)HiCParser_1.5.1.tgz(r-4.5-x86_64)HiCParser_1.5.1.tgz(r-4.5-arm64)
HiCParser_1.5.1.tar.gz(r-4.7-arm64)HiCParser_1.5.1.tar.gz(r-4.7-x86_64)HiCParser_1.5.1.tar.gz(r-4.6-arm64)HiCParser_1.5.1.tar.gz(r-4.6-x86_64)
HiCParser_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HiCParser/json (API)

# Install 'HiCParser' in R:

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

Bug tracker:https://github.com/emaigne/hicparser/issues

Uses libs:

zlib– Compression library
c++– GNU Standard C++ Library v3

On BioConductor:HiCParser-1.5.1(bioc 3.24)HiCParser-1.4.0(bioc 3.23)

software hic dataimport zlib cpp

5.43 score 1 stars 2 packages 1 scripts 261 downloads 5 exports 22 dependencies

Last updated from:84b40db8cc. Checks:14 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	162
linux-devel-arm64	NOTE	196
linux-devel-x86_64	NOTE	290
source / vignettes	OK	228
linux-release-arm64	NOTE	195
linux-release-x86_64	NOTE	259
macos-release-arm64	NOTE	182
macos-release-x86_64	NOTE	444
macos-oldrel-arm64	NOTE	187
macos-oldrel-x86_64	NOTE	309
windows-devel-arm64	NOTE	292
windows-devel-x86_64	NOTE	245
windows-release-arm64	NOTE	297
windows-release-x86_64	NOTE	198
windows-oldrel-x86_64	NOTE	185
wasm-release	OK	110

Exports:mergeInteractionSet parseCool parseHiC parseHiCPro parseTabular

Dependencies:abind Biobase BiocGenerics data.table DelayedArray generics GenomicRanges gtools InteractionSet IRanges lattice Matrix MatrixGenerics matrixStats pbapply Rcpp S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment XVector

Introduction to HiCParser

Rendered fromHiCParser.Rmdusingknitr::rmarkdown

Last update: 2024-11-06
Started: 2024-07-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A multiple format Hi-C data parser	HiCParser-package HiCParser
Merge two InteractionSet objects	mergeInteractionSet
Parser for data in cool format	parseCool
Parser for data in hic format	parseHiC
Parser for HiCPro data	parseHiCPro
Parser for tabular data	parseTabular