ArticleBMC bioinformatics2019
CAGEfightR: analysis of 5'-end data using R/Bioconductor.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.Nature communications · 2026Article
- G-quadruplex structures as modulators of alternative promoter usage.NAR genomics and bioinformatics · 2025Article
- Interaction Between Enhancers and Promoters in Chicken Genome.International journal of molecular sciences · 2025Article
- Alternative transcription increases isoform complexity in Long Non-Coding RNAs and alters their functions in cancer.Non-coding RNA research · 2025Review
- True length of diverse capped RNA sequencing (TLDR-seq): 5'-3'-end sequencing of capped RNAs regardless of 3'-end status.Nucleic acids research · 2025Article
- Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing.PloS one · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- Transcription termination and readthrough in African swine fever virus.Frontiers in immunology · 2024Article
- Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases.Genes · 2023Review
- Identification of herpesvirus transcripts from genomic regions around the replication origins.Scientific reports · 2023Article
- Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.G3 (Bethesda, Md.) · 2023Article
- Article
- CAGE sequencing reveals CFTR-dependent dysregulation of type I IFN signaling in activated cystic fibrosis macrophages.Science advances · 2023Article
- Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation.Molecular and cellular biology · 2023Article
- Article
- Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis.Nature communications · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
background5'-end sequencing assays, and Cap Analysis of Gene Expression (CAGE) in particular, have been instrumental in studying transcriptional regulation. 5'-end methods provide genome-wide maps of transcription start sites (TSSs) with base pair resolution. Because active enhancers often feature bidirectional TSSs, such data can also be used to predict enhancer candidates. The current availability of mature and comprehensive computational tools for the analysis of 5'-end data is limited, preventing efficient analysis of new and existing 5'-end data.
resultsWe present CAGEfightR, a framework for analysis of CAGE and other 5'-end data implemented as an R/Bioconductor-package. CAGEfightR can import data from BigWig files and allows for fast and memory efficient prediction and analysis of TSSs and enhancers. Downstream analyses include quantification, normalization, annotation with transcript and gene models, TSS shape statistics, linking TSSs to enhancers via co-expression, identification of enhancer clusters, and genome-browser style visualization. While built to analyze CAGE data, we demonstrate the utility of CAGEfightR in analyzing nascent RNA 5'-data (PRO-Cap). CAGEfightR is implemented using standard Bioconductor classes, making it easy to learn, use and combine with other Bioconductor packages, for example popular differential expression tools such as limma, DESeq2 and edgeR.
conclusionsCAGEfightR provides a single, scalable and easy-to-use framework for comprehensive downstream analysis of 5'-end data. CAGEfightR is designed to be interoperable with other Bioconductor packages, thereby unlocking hundreds of mature transcriptomic analysis tools for 5'-end data. CAGEfightR is freely available via Bioconductor: bioconductor.org/packages/CAGEfightR .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.