To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("HiTC")
In most cases, you don't need to download the package archive at all.
HiTC
High Throughput Chromosome Conformation Capture analysis
Bioconductor version: 3.0
The HiTC package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.
Author: Nicolas Servant
Maintainer: Nicolas Servant <nicolas.servant at curie.fr>
Citation (from within R,
enter citation("HiTC")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("HiTC")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HiTC")
| R Script | Hight-Throughput Chromosome Conformation Capture analysis | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | HighThroughputSequencing, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15.0), methods, IRanges, GenomicRanges |
| Imports | Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix |
| LinkingTo | |
| Suggests | BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | HiCDataHumanIMR90 |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | HiTC_1.10.0.tar.gz |
| Windows Binary | HiTC_1.10.0.zip |
| Mac OS X 10.6 (Snow Leopard) | HiTC_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | HiTC_1.10.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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