SUMMARY: MicroRNAs (miRNAs) function as master regulators of gene expression. Recent studies demonstrate that miRNA isoforms (isomiRs) play a unique role in cancer development. Here, we present QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designed for the detection and annotation of heterogeneous isomiRs, it permits extensive customization of the query process and reference databases to meet the user 's diverse research needs. AVAILABILITY AND IMPLEMENTATION: QuagmiR is written in Python and can be obtained freely from GitHub (https://github.com/Gu-Lab-RBL-NCI/QuagmiR). QuagmiR can be run from the command line on local machines, as well as on high-performance servers. A web-accessible version of the tool has also been made available for use by academic researchers through the National Cancer Institute-funded Seven Bridges Cancer Genomics Cloud (https://cancergenomicscloud.org). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.
SUMMARY: MicroRNAs (miRNAs) function as master regulators of gene expression. Recent studies demonstrate that miRNA isoforms (isomiRs) play a unique role in cancer development. Here, we present QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designed for the detection and annotation of heterogeneous isomiRs, it permits extensive customization of the query process and reference databases to meet the user 's diverse research needs. AVAILABILITY AND IMPLEMENTATION: QuagmiR is written in Python and can be obtained freely from GitHub (https://github.com/Gu-Lab-RBL-NCI/QuagmiR). QuagmiR can be run from the command line on local machines, as well as on high-performance servers. A web-accessible version of the tool has also been made available for use by academic researchers through the National Cancer Institute-funded Seven Bridges Cancer Genomics Cloud (https://cancergenomicscloud.org). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.
Authors: Ryan D Morin; Michael D O'Connor; Malachi Griffith; Florian Kuchenbauer; Allen Delaney; Anna-Liisa Prabhu; Yongjun Zhao; Helen McDonald; Thomas Zeng; Martin Hirst; Connie J Eaves; Marco A Marra Journal: Genome Res Date: 2008-02-19 Impact factor: 9.043
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Authors: Thomas Desvignes; Phillipe Loher; Karen Eilbeck; Jeffery Ma; Gianvito Urgese; Bastian Fromm; Jason Sydes; Ernesto Aparicio-Puerta; Victor Barrera; Roderic Espín; Florian Thibord; Xavier Bofill-De Ros; Eric Londin; Aristeidis G Telonis; Elisa Ficarra; Marc R Friedländer; John H Postlethwait; Isidore Rigoutsos; Michael Hackenberg; Ioannis S Vlachos; Marc K Halushka; Lorena Pantano Journal: Bioinformatics Date: 2020-02-01 Impact factor: 6.937