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Cap analysis of gene expression bioinformatics software tools

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…
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HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

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CAGEr
Desktop

CAGEr

Provides a comprehensive toolbox for analysis and visualization of CAGE (Cap…

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…

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PEDAL
Desktop

PEDAL Promoter-Enhancer Discriminative AnaLysis

A computational framework for distinguishing effectively transcriptional…

A computational framework for distinguishing effectively transcriptional profiles of promoters and enhancers. PEDAL uses solely histone modification marks, chromatin accessibility and binding sites…

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Heat*seq
Web
Desktop

Heat*seq

A web-tool that allows genome scale comparison of high throughput experiments…

A web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq allows users to contextualise…

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CAGEd-oPOSSUM
Web
Desktop

CAGEd-oPOSSUM

A web-based system for the detection of over-represented transcription factor…

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…

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CAGEscan-Cluste…
Desktop

CAGEscan-Clustering

Creates transcript assemblies from CAGEScan derived Transcription Start Site…

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.…

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piPipes
Desktop

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…

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CAGExploreR
Desktop

CAGExploreR

An R package to detect and visualize changes in the use of specific TSS in…

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…

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CapFilter
Desktop

CapFilter

A straightforward annotation-agnostic computational pipeline that greatly…

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…

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RECLU
Desktop

RECLU

A reproducible clustering pipeline with multiple scales using capped analysis…

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…

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TomeTools
Desktop

TomeTools

A collection of programs to store and manipulate thousands of CAGE datasets.…

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.

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MOIRAI
Desktop

MOIRAI

A compact yet flexible workflow system designed to carry out the main steps in…

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,…

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