FunChIP
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This is the development version of FunChIP; for the stable release version, see FunChIP.
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Bioconductor version: Development (3.19)
Preprocessing and smoothing of ChIP-Seq peaks and efficient implementation of the k-mean alignment algorithm to classify them.
Author: Alice Parodi [aut, cre], Marco Morelli [aut, cre], Laura M. Sangalli [aut], Piercesare Secchi [aut], Simone Vantini [aut]
Maintainer: Alice Parodi <alicecarla.parodi at polimi.it>
citation("FunChIP")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("FunChIP")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ChIPSeq, Clustering, Software, StatisticalMethod |
| Version | 1.29.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2), GenomicRanges |
| Imports | shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/FunChIP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FunChIP |
| Package Short Url | https://bioconductor.org/packages/FunChIP/ |
| Package Downloads Report | Download Stats |