CAGEr-package: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing...
In ge11232002/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Description
CAGEr package performs identification of transcription start sites and frequency of their usage from input CAGE sequencing data, normalization of raw CAGE tag count, clustering of TSSs into tag clusters (TC) and their aggregation across multiple CAGE experiments to construct the promoterome. It manipulates multiple CAGE experiments at once, performs expression profiling across experiments both at level of individual TSSs and clusters of TSSs, exports several different types of track files for visualization in the UCSC Genome Browser, performs analysis of promoter width and detects differential usage of TSSs (promoter shifting) between samples. Multicore option for parallel processing is supported on Unix-like platforms.
Details
Package: CAGEr
Type: Package
Version: 1.0
Date: 2012-12-18
License: GPL-3
Depends: R (>= 2.15.0), methods, BSgenome
Author(s)
Vanja Haberle
Maintainer: Vanja Haberle <vanja.haberle@bio.uib.no>
ge11232002/CAGEr documentation built on May 17, 2019, 12:13 a.m.
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Description
CAGEr package performs identification of transcription start sites and frequency of their usage from input CAGE sequencing data, normalization of raw CAGE tag count, clustering of TSSs into tag clusters (TC) and their aggregation across multiple CAGE experiments to construct the promoterome. It manipulates multiple CAGE experiments at once, performs expression profiling across experiments both at level of individual TSSs and clusters of TSSs, exports several different types of track files for visualization in the UCSC Genome Browser, performs analysis of promoter width and detects differential usage of TSSs (promoter shifting) between samples. Multicore option for parallel processing is supported on Unix-like platforms.
Details
| Package: | CAGEr |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2012-12-18 |
| License: | GPL-3 |
| Depends: | R (>= 2.15.0), methods, BSgenome |
Author(s)
Vanja Haberle
Maintainer: Vanja Haberle <vanja.haberle@bio.uib.no>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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