Re: UTAP
On 31/03/2019 12:51, Marilyn Safran wrote:
Hi Tony,
Feel free to try out the software without using a docker container,
and prepare and distribute the Debian-Med package.
Please let us know when that package becomes available, and how to
access it.
And please make sure to acknowledge our paper so that others can
contact us if needed.
Hi, Marilyn.
The first step is for me to let the Debian-Med team know about UTAP, by
CC to the Debian-Med mailing list, and for me to try it without using a
Docker container to see what other software dependencies UTAP requires.
@debian-med list,
I'm interested in packaging UTAP:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2728-2
UTAP: User-friendly Transcriptome Analysis Pipeline
RNA-Seq technology is routinely used to characterize the transcriptome,
and to detect gene expression differences among cell types, genotypes
and conditions. Advances in short-read sequencing instruments such as
Illumina Next-Seq have yielded easy-to-operate machines, with high
throughput, at a lower price per base. However, processing this data
requires bioinformatics expertise to tailor and execute specific
solutions for each type of library preparation. In order to enable fast
and user-friendly data analysis, we developed an intuitive and scalable
transcriptome pipeline that executes the full process, starting from
cDNA sequences derived by RNA-Seq [Nat Rev Genet 10:57-63, 2009] and
bulk MARS-Seq [Science 343:776-779, 2014] and ending with sets of
differentially expressed genes. Output files are placed in structured
folders, and results summaries are provided in rich and comprehensive
reports, containing dozens of plots, tables and links. Our User-friendly
Transcriptome Analysis Pipeline (UTAP) is an open source, web-based
intuitive platform available to the biomedical research community,
enabling researchers to efficiently and accurately analyse transcriptome
sequence data.
The software is available under GPLv3:
https://utap.readthedocs.io/en/latest/
I've contacted the upstream authors Refael Kohen, Dena Leshkowitz, and
Marilyn Safran who are willing to let us package and distribute their
UTAP software for Debian-Med.
Thanks,
Tony.
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