CAGEr-package: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing...
In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Description
The 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.
Author(s)
Vanja Haberle
CAGEr documentation built on Jan. 17, 2021, 2 a.m.
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Description
The 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.
Author(s)
Vanja Haberle
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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