Article

SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis

2025-08-21

Abstract excerpt

<h4>Background</h4> Alternative promoter usage regulates isoform diversity in mammals, playing critical roles in development, disease, and cellular reprogramming. While Cap Analysis of Gene Expression (CAGE) enables precise transcription start site mapping, its high cost and limited coverage hinder scalability. In contrast, RNA-seq is abundant across biological contexts; several algorithms (ProActiv, Salmon, DEXS...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: dfff5191-82e9-557e-9361-bece211cab08
DOI: 10.1101/2025.08.16.669128

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

SnakeAltPromoter Facilitates Differential Alternative Promoter AnalysisDOI 10.1101/2025.08.16.669128Read

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative PromotersSemantic proximity Read

Expression and Splicing Mediate Distinct Biological SignalsSemantic proximity Read

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversitySemantic proximity Read

<i>SplAdder</i> : Identification, quantification and testing of alternative splicing events from RNA-Seq dataSemantic proximity Read

Analysis of alternative polyadenylation from long-read or short-read RNA-seq with LAPASemantic proximity Read

Identification and quantification of alternative polyadenylation sites in single cell RNA-seq data using scPAISOSemantic proximity Read

STARRPeaker: Uniform processing and accurate identification of STARR-seq active regionsSemantic proximity Read

Predicting the Impact of cis-Regulatory Variation on Alternative PolyadenylationSemantic proximity Read

The Junction Usage Model (JUM): A method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patternsSemantic proximity Read

Pervasive co-regulation of alternative splicing with transcription initiation and termination.Semantic proximity Read

Quantification of single cell-type-specific alternative transcript initiationSemantic proximity Read

Improved detection of genetic effects on promoter usage with augmented transcript annotationsSemantic proximity Read