Cap analysis of gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. By the large-scale analysis of 5' end of transcripts using CAGE method, it enables not only determination of the transcription start site but also prediction of promoter region. Source text: Murata et al., 2014.
CAGEd-oPOSSUM
CAGEd-oPOSSUM
A web-based system for the detection of over-represented transcription factor binding…
A web-based system for the detection of over-represented transcription factor binding sites around CAGE peaks. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived cis-regulatory regions, CAGEd-oPOSSUM can…
CAGEr
CAGEr
Provides a comprehensive toolbox for analysis and visualization of CAGE (Cap Analysis of…
Provides a comprehensive toolbox for analysis and visualization of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites (TSS) and promoterome mining in R. CAGEr performs identification of…
CAGEscan-Clustering
CAGEscan-Clustering
Creates transcript assemblies from CAGEScan derived Transcription Start Site (TSS)…
Creates transcript assemblies from CAGEScan derived Transcription Start Site (TSS) associated reads paired with randomly primed readsm, grouping them on the basis of the common location of TSS reads. Assembly-seeding TSS read clusters can either be…
CAGExploreR
CAGExploreR
An R package to detect and visualize changes in the use of specific TSS in wider promoter…
An R package to detect and visualize changes in the use of specific TSS in wider promoter regions in the context of changes in overall gene expression when comparing different CAGE samples. These changes provide insight into the modification of…
CapFilter
CapFilter
A straightforward annotation-agnostic computational pipeline that greatly increases…
A straightforward annotation-agnostic computational pipeline that greatly increases confidence in predicted transcription start sites (TSSs) and allows tuning by the end-user to balance both precision and sensitivity of TSS identification to address…
MOIRAI
MOIRAI
A compact yet flexible workflow system designed to carry out the main steps in data…
A compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the…
piPipes
piPipes
A coordinated set of pipelines, 'piPipes', to analyze piRNA and…
A coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression…
RECLU
RECLU
A reproducible clustering pipeline with multiple scales using capped analysis of gene…
A reproducible clustering pipeline with multiple scales using capped analysis of gene expression (CAGE). RECLU discoveries numerous alternative transcription start sites (TSSs) with the biological implication for your sample.
TomeTools
TomeTools
A collection of programs to store and manipulate thousands of CAGE datasets. The core of…
A collection of programs to store and manipulate thousands of CAGE datasets. The core of TomeTools is a database to store nucleotide resolution NGS coverage data.