Ballgown pipeline

Ballgown specifications

Information


Unique identifier OMICS_11745
Name Ballgown
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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Maintainer


  • person_outline Jeffrey Leek <>

Publication for Ballgown

Ballgown IN pipelines

 (5)
2018
PMCID: 5895686
PMID: 29417162
DOI: 10.1007/s00122-018-3065-y

[…] age{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\bf{y}} = {\bf{xb}} + {\boldsymbol \varepsilon}$$\end{document}y=xb+ε using ballgown (frazee et al. 2015) where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \u […]

2017
PMCID: 5601427
PMID: 28916800
DOI: 10.1038/s41598-017-12020-3

[…] 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 […]

2017
PMCID: 5678563
PMID: 29115926
DOI: 10.1186/s12870-017-1143-y

[…] time points or not, 17 rnaseq samples covering those published and our rnaseq data of cd-treated rice seedling roots (additional file 1: table s1) were processed by the new pipeline hisat-stringtie-ballgown. after filtering those transcripts with no more than 50% missing data, 22,080 transcripts across 17 rnaseq samples (additional file 8: dataset 2) were selected for analysis of degs […]

2017
PMCID: 5821214
PMID: 29143824
DOI: 10.1038/nature24649

[…] prjna285408)6 and the european genome-phenome archive2. reads were extracted in fasta format from sra or bam files and aligned to the hg19 genome with hisat230 and processed with stringtie31 and ballgown32. all samples with available genomic data (wes or wgs) were included in the analysis. using gsva37 for each sample, an enrichment score was calculated based on the gene set […]

2016
PMCID: 5354857
PMID: 27992366
DOI: 10.18632/oncotarget.13948

[…] analyses were based on the high quality clean data. the clean reads were aligned to the human genome (version: grch37) using the hisat2 program (v2-2.0.1) [47, 48]. we applied stringtie (v1.3.0) and ballgown algorithms to identify the significantly differentially expressed genes using the following criteria: fc > 2.0 or < 0.5, p < 0.05 and fdr < 0.1. scatter and volcano plots […]

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)
Supported by US National Institutes of Health 1R01GM105705, and a Hopkins Sommer Scholarship.

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