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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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  • person_outline Jeffrey Leek <>

Publication for Ballgown

Ballgown in pipelines

 (4)
2017
PMCID: 5567338
PMID: 28831078
DOI: 10.1038/s41598-017-08738-9

[…] the quantification of lncrnas and mrnas in each sample was calculated by stringtie. differentially expressed mrnas and lncrnas between low and high sperm motility groups was analyzed using the ballgown (2.6.0) r package. p-value < 0.05 and |fold-change| > 1.5 were considered as significance threshold. go enrichment analysis of differentially expressed mrnas and lncrnas were performed […]

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 : 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 : dataset 2) were selected for analysis of degs […]

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

[…] prjna285408) and the european genome-phenome archive. reads were extracted in fasta format from sra or bam files and aligned to the hg19 genome with hisat2 and processed with stringtie and ballgown. all samples with available genomic data (wes or wgs) were included in the analysis. using gsva for each sample, an enrichment score was calculated based on the gene set […]


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Ballgown in publications

 (25)
PMCID: 5841368
PMID: 29515098
DOI: 10.1038/s41419-018-0382-7

[…] rna assay kit in a qubit® 2.0 fluorometer (life technologies, ca, usa). rna integrity was assessed using a rna nano 6000 assay kit and a bioanalyzer 2100 system (agilent technologies, ca, usa). the ballgown suite includes functions for the interactive exploration of the transcriptome assembly, visualisation of transcript structures, an abundance of features specific for each locus, and post hoc […]

PMCID: 5828519
PMID: 29444188
DOI: 10.1371/journal.ppat.1006861

[…] was performed using the new tuxedo pipeline[]. the clean reads were aligned to the human genome (version: grch38) using the hisat2 program (v2-2.0.1). we applied stringtie (version 0.36) and ballgown algorithms to identify the significantly differentially expressed genes (p<0.05). cytokine, chemokine and their receptors gene expression was extracted from the differential gene […]

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. ) where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepa […]

PMCID: 5933896
PMID: 29401570
DOI: 10.4062/biomolther.2017.240

[…] variants for each gene locus. stringtie estimates gene-level measurements by appropriately combining fragments per kilobase of exon per million reads (fpkms) from the transcripts of each gene., ballgown () is a bioconductor-based suite that hosts a comprehensive set of bioconductor communities. the “stattest” function of ballgown is available with a gene feature that prevents data skewing […]

PMCID: 5758543
PMID: 29354151
DOI: 10.3389/fpls.2017.02215

[…] samtools (). based on the alignments, transcript abundances were estimated and transcript assembly was performed using the stringtie () program. deg analysis was carried out using the r package ballgown ()., the expression level of selected degs identified from rna-seq data were validated by qrt-pcr using the cdna samples used for rna-seq library construction. the primer pairs […]


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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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