UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline DOI Creative Commons
J Lindner, Bareket Dassa, Noa Wigoda

et al.

BMC Bioinformatics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 7, 2025

Abstract Background The emergence of next-generation sequencing (NGS) marked a revolution in biological research, enabling comprehensive characterization the transcriptome and detailed analysis epigenome landscape. This technology has made it possible to detect differences across cell types, genotypes, conditions. Advances short-read platforms, have produced user-friendly machines that offer high throughput at reduced cost per base. However, leveraging this data still requires bioinformatics expertise develop execute tailored solutions for each specific application. Democratizing access sequence tools is crucial empower researchers from diverse fields harness full potential NGS data. Results UTAP2, our enhanced version UTAP published 2019 (Kohen et al. BMC Bioinform 20(1):154, 2019), empowers unlock mysteries gene expression epigenetic modifications with ease. user-friendly, open-source pipeline, built by unit programmers deep analysts, streamlines analysis, handling everything sequences or peak counts differentially expressed genes genomic regions annotation. are delivered organized folders rich reports packed plots, tables, links effortless interpretation. Since debut UTAP, been embraced many Weizmann Institute over 100 citations, thus highlighting its scientific contribution. Conclusion Our User-friendly Transcriptome Epigenome Analysis Pipeline UTAP2 available broader biomedical research community as an installation. With single image, can be installed on both local servers cloud allowing users leverage parallel cluster resources. Once enables researchers, even those limited skills efficiently, accurately reliably analyse

Language: Английский

UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline DOI Creative Commons
J Lindner, Bareket Dassa, Noa Wigoda

et al.

BMC Bioinformatics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 7, 2025

Abstract Background The emergence of next-generation sequencing (NGS) marked a revolution in biological research, enabling comprehensive characterization the transcriptome and detailed analysis epigenome landscape. This technology has made it possible to detect differences across cell types, genotypes, conditions. Advances short-read platforms, have produced user-friendly machines that offer high throughput at reduced cost per base. However, leveraging this data still requires bioinformatics expertise develop execute tailored solutions for each specific application. Democratizing access sequence tools is crucial empower researchers from diverse fields harness full potential NGS data. Results UTAP2, our enhanced version UTAP published 2019 (Kohen et al. BMC Bioinform 20(1):154, 2019), empowers unlock mysteries gene expression epigenetic modifications with ease. user-friendly, open-source pipeline, built by unit programmers deep analysts, streamlines analysis, handling everything sequences or peak counts differentially expressed genes genomic regions annotation. are delivered organized folders rich reports packed plots, tables, links effortless interpretation. Since debut UTAP, been embraced many Weizmann Institute over 100 citations, thus highlighting its scientific contribution. Conclusion Our User-friendly Transcriptome Epigenome Analysis Pipeline UTAP2 available broader biomedical research community as an installation. With single image, can be installed on both local servers cloud allowing users leverage parallel cluster resources. Once enables researchers, even those limited skills efficiently, accurately reliably analyse

Language: Английский

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