ArticlebioRxiv : the preprint server for biology2026
REPLAY: A reproducible and user-friendly application for DNA replication timing analysis from Repli-seq data.
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Background: DNA replication timing (RT) is a fundamental feature of genome organization that is regulated in a cell-type-specific manner and frequently altered in disease. Repli-seq is the standard approach for genome-wide RT profiling; however, its analysis typically requires multiple independent tools and custom scripts, limiting reproducibility, portability, and accessibility, particularly for users without computational expertise. In addition, existing workflows often lack standardization and require substantial user intervention. Results: We developed REPLAY, a fully automated, reproducible, and user-friendly application for replication timing analysis. REPLAY is distributed as a standalone executable that enables end-to-end processing from compressed FASTQ files to genome-wide RT profiles without requiring software installation or programming experience. Through an intuitive graphical interface, users can configure analysis parameters, including input and output directories, reference genome, normalization strategy (quantile, median, or interquartile range), and smoothing. The application integrates all processing steps-quality control, trimming, alignment, binning, RT log2 calculation, normalization, smoothing, and visualization-within a single automated workflow. Application of REPLAY to publicly available datasets demonstrate accurate reconstruction of RT profiles and high reproducibility across samples. Conclusions: REPLAY offers a portable, reproducible, and accessible solution for the analysis of RT data. By eliminating the need for command-line tools and complex installations, it lowers the entry barrier enabling standardized analysis across diverse research settings.
Indexed as
Identifiers
What OpenQuestion holds
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.