From 68629c9af46ccad1d41ef59fe9cc563b5c57c2cf Mon Sep 17 00:00:00 2001 From: Siddharth Sethi Date: Tue, 6 Jan 2026 10:34:23 +0000 Subject: [PATCH] updating psqan's citation --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 97791bd..8ad2072 100644 --- a/README.md +++ b/README.md @@ -29,10 +29,13 @@ - [Ranked transcripts](#ranked-transcripts) - [Other useful commands](#other-useful-commands) - [Licence](#licence) +- [Citing PSQAN](#citing-psqan) ## Overview +> **_Publication:_** *Bioinformatics Advances (2025)*. DOI: https://doi.org/10.1093/bioadv/vbaf293 + ## Introduction Despite the advances in tools to process long-read RNA-sequencing (lrRNA-seq) data, the downstream analysis of transcriptional data remains challenging due to the detection of thousands of novel transcripts and the lack of tools to prioritise functionally important transcripts. From such a large number of transcripts, it is difficult to distinguish between stable transcripts of potential biological importance, partially processed RNAs and splicing noise. Furthermore, when using lrRNA-seq to identify rare and novel transcripts, the recommendation is to incorporate multiple replicates in the study design and implement transcript-level filters. However, determining optimal expression thresholds for filtering and selecting transcripts which are reproducible across samples remains a significant challenge. Consequently, researchers find it challenging to interpret lrRNA-seq data effectively and generate relevant hypothesis which could be experimentally validated in the laboratory. @@ -237,4 +240,9 @@ Copyright 2024 Astex Therapeutics Ltd. This repository is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -This repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the [LICENSE](LICENSE) file (GNU General Public License) for more details. \ No newline at end of file +This repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the [LICENSE](LICENSE) file (GNU General Public License) for more details. + +## Citing PSQAN +If you use PSQAN in your research, please cite the following publication: https://doi.org/10.1093/bioadv/vbaf293 + +Siddharth Sethi, Emil K Gustavsson, Harpreet Saini, Mina Ryten, PSQAN: a pipeline to prioritize novel and biologically relevant transcripts from long-read RNA sequencing, Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf293, https://doi.org/10.1093/bioadv/vbaf293 \ No newline at end of file