FunChIP
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see FunChIP.
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Bioconductor version: 3.9
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 "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("FunChIP")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("FunChIP")| An introduction to FunChIP | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, Clustering, Software, StatisticalMethod |
| Version | 1.10.0 |
| 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 | FunChIP_1.10.0.tar.gz |
| Windows Binary | FunChIP_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | FunChIP_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/FunChIP |
| Source Repository (Developer Access) | git clone [email protected]:packages/FunChIP |
| Bioc Package Browser | https://code.bioconductor.org/browse/FunChIP/ |
| Package Short Url | https://bioconductor.org/packages/FunChIP/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |