Ballgown specifications

Information


Unique identifier OMICS_11745
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Align reads and assemble transcripts
Input format BAM, GTF
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Stability Stable
Source code URL https://codeload.github.com/alyssafrazee/ballgown/zip/master
Maintained Yes

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Documentation


Maintainer


  • person_outline Jeffrey Leek <>

Ballgown article

Ballgown citation

2017
PMCID: 5601427

[…] 3 , rna-seq is generally used to determine which genes are up- or down-regulated by comparing gene expression levels between conditions, such as drought stress treatment vs non-treated. we used ballgown to identify dets between each treatment and variety from the expression estimates computed in the tophat-stringtie pipeline. the breeding parent hanfengb under the ww condition was taken […]

Ballgown institution(s)
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Ballgown funding source(s)
This work was partially supported by US National Institutes of Health 1R01GM105705 and by a Hopkins Sommer Scholarship.

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