lncRNA-screen statistics

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Citations per year

Number of citations per year for the bioinformatics software tool lncRNA-screen
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lncRNA-screen specifications

Information


Unique identifier OMICS_14314
Name lncRNA-screen
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A list of Sequence Read Archive (SRA) accession numbers or The Cancer Genome Atlas (TCGA) UUIDs matched with user-defined sample names.
Output data An interactive lncRNA report.
Output format HTML, XLS
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Aristotelis Tsirigos

Additional information


https://github.com/NYU-BFX/lncRNA-screen/blob/master/README.md

Publication for lncRNA-screen

lncRNA-screen citations

 (2)
library_books

Elucidating the Role of Host Long Non Coding RNA during Viral Infection: Challenges and Paths Forward

2017
PMCID: 5748604
PMID: 29053596
DOI: 10.3390/vaccines5040037

[…] s are needed from the same experimental systems in order to extract predictive features for inferring lncRNA functions. We anticipate that as large scale perturbation techniques mature, some of these lncRNA screen studies will emerge as initial training datasets. Obviously, given the complexities of different high-throughput technologies, developing benchmark training datasets for this purpose req […]

library_books

lncRNA screen: an interactive platform for computationally screening long non coding RNAs in large genomics datasets

2017
BMC Genomics
PMCID: 5458484
PMID: 28583068
DOI: 10.1186/s12864-017-3817-0

[…] To demonstrate the flexibility of our pipeline we integrated RNA-seq/ChIP-seq data from Roadmap Epigenomics with matched Hi-C data from a previous study [, ]. First, we rerun the lncRNA-screen pipeline focusing only on the samples that have matched Hi-C data (the report is included in GitHub). For each cell type, we defined expressed mRNAs, lncRNAs including annotated and nove […]


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lncRNA-screen institution(s)
Department of Pathology, New York University School of Medicine, New York, NY, USA; NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY, USA; Department of Population Health, New York University School of Medicine, NY, USA; Goldman Sachs Group Inc, New York, NY, USA; Applied Bioinformatics Center, Office of Collaborative Science, New York University School of Medicine, NY, USA
lncRNA-screen funding source(s)
The study was supported by a Research Scholar Grant, RSG-15-189-01 - RMC from the American Cancer Society and the research program R01CA194923 and R01CA169784 from National Institute of Health (National Cancer Institute).

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