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Protocols

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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Documentation


Maintainer


  • person_outline Jeffrey Leek

Publication for Ballgown

Ballgown citations

 (18)
library_books

Single and multiple phenotype QTL analyses of downy mildew resistance in interspecific grapevines

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

[…] l. ) and the transcriptome was assembled using StringTie (Pertea et al. ) with the CRIBI functional annotation (Vitulo et al. ). Transcribed genes were analyzed by fitting a linear model y=Xb+ε using Ballgown (Frazee et al. ) where y was a vector holding the log2(FPKM + 1) values of genes with FPKM (Fragments Per Kilobase of transcript per Million reads sequenced) variances greater than one for ea […]

library_books

Construction of a Transcriptome Driven Network at the Early Stage of Infection with Influenza A H1N1 in Human Lung Alveolar Epithelial Cells

2018
PMCID: 5933896
PMID: 29401570
DOI: 10.4062/biomolther.2017.240

[…] 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 in […]

call_split

Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach (Prunus persica)

2018
Front Plant Sci
PMCID: 5758543
PMID: 29354151
DOI: 10.3389/fpls.2017.02215
call_split See protocol

[…] using 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 (). […]

library_books

PD 1 is a haploinsufficient suppressor of T cell lymphomagenesis

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

[…] (Illumina, San Diego, California, USA). Read alignment to the mm10 genome and transcriptome assembly were performed using HISAT2 and StringTie, respectively. Differential expression was assessed with Ballgown. GSEA was performed with BubbleGUM; to assess proliferation, the following signatures were selected: Whitfield_cell_cycle_literature, Ishida_E2F_targets and Hallmark_G2M_checkpoint. RNAseq da […]

library_books

Co expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium responsive genes

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

[…] A comprehensive analysis pipeline was formulated and our workflow for analysis of RNAseq data was illustrated in Fig. . In brief, two ‘Tuxedo’ packages, TopHat-Cufflinks [] and HISAT-StringTie-Ballgown [], were utilized in parallel to process the RNAseq data and output per kilobase transcript per million reads mapped (FPKM) matrix for differential expression analysis (Fig. ). The rice refer […]

library_books

The association between DNA methylation and exon expression in the Pacific oyster Crassostrea gigas

2017
PLoS One
PMCID: 5612690
PMID: 28945769
DOI: 10.1371/journal.pone.0185224

[…] .3 package [] processes the read alignments and the reference annotation with parameters setting “-eB”. Using this input, StringTie estimates abundances and creates new transcript tables for input to Ballgown. Gene expression levels were measured using FPKM calculated using R package Ballgown []. […]

Citations

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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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