Skip to content

CAGEr

Bioc current

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

v2.18.0 · software · GPL-3
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.12 · Apr 4, 2013

Current · Requires R 4.6

1.0 In 27 of 49 releases 3.23

Description

The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.

Code

Code metrics have not been computed for this package yet.

Topics

Software › WorkflowStep › Preprocessing
Software › Technology › Sequencing
Software › WorkflowStep › Normalization
Software › ResearchField › FunctionalGenomics
Software › AssayDomain › Transcription
Software › AssayDomain › GeneExpression
Software › StatisticalMethod › Clustering
Software › WorkflowStep › Visualization

Depended on by (2)

Bioconductor (2)

seqPattern seqArchRplus

People