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
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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-1.5.0(bioc 3.24)HiCParser-1.4.0(bioc 3.23)

software hic dataimport zlib cpp

5.56 score 1 stars 2 packages 1 scripts 234 downloads 5 exports 22 dependencies

Last updated from:84b40db8cc. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	179
linux-devel-arm64	NOTE	248
linux-devel-x86_64	NOTE	268
source / vignettes	OK	239
linux-release-arm64	NOTE	223
linux-release-x86_64	NOTE	267
macos-release-arm64	NOTE	163
macos-release-x86_64	NOTE	463
macos-oldrel-arm64	NOTE	135
macos-oldrel-x86_64	NOTE	404
windows-devel	NOTE	244
windows-release	NOTE	200
windows-oldrel	NOTE	205
wasm-release	OK	155

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