CummeRbund statistics

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CummeRbund specifications

Information


Unique identifier OMICS_07349
Name CummeRbund
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.7.2
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Loyal Goff

Publication for CummeRbund

CummeRbund citations

 (296)
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The local microenvironment limits the regenerative potential of the mouse neonatal heart

2018
Sci Adv
PMCID: 5931766
PMID: 29732402
DOI: 10.1126/sciadv.aao5553
call_split See protocol

[…] using TopHat v2.0.143. Following mapping, the transcript and normalization counts were performed using Cuffdiff v2.2.1 4. The differential expression analysis of normalized counts was performed using cummeRbund v2.12 5, a widely used R v3.2 package that works together with the Cuffdiff software; the applied threshold on the parameter α in the function getSig of the package was ≤0.05. Last, the dif […]

call_split

EZH2 inhibitors sensitize myeloma cell lines to panobinostat resulting in unique combinatorial transcriptomic changes

2018
Oncotarget
PMCID: 5955152
PMID: 29774113
DOI: 10.18632/oncotarget.25128
call_split See protocol

[…] cate. Sequencing data was subjected to quality control analysis (FastQC), processed (FASTQ and Tophat2(aligned to hg19)), analyzed for differential expression (Cufflinks and Cuffdiff) and visualized (CummeRbund) using the open source, web-based platform Galaxy []. Downstream subsetting and analysis was conducted using the R programing language and Ingenuity Pathway Analysis (IPA; QIAGEN; Venlo, Ne […]

library_books

Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

2018
PLoS One
PMCID: 5908059
PMID: 29672525
DOI: 10.1371/journal.pone.0194792

[…] (Bowtie2.1.0, TopHat2.0.9 [], Cufflinks 2.2.1 [], Cuffmerge 2.2.1, CuffDiff 2.2.1) mapped to the Pisifera 5 reference genome build assembly and linked to 26,059 gene model []. The R package library, Cummerbund, was used to plot heatmaps of significant differentially expressed R genes and FA genes generated by CuffDiff. RNA-seq data from kernel and mesocarp tissues were read mapped using the Tuxed […]

library_books

Low input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex

2018
Sci Adv
PMCID: 5906078
PMID: 29675472
DOI: 10.1126/sciadv.aar8187

[…] Sequencing reads were trimmed by Trim Galore! with default settings. The trimmed reads were aligned by TopHat () and further analyzed by cufflinks (). Gene expression levels were plotted by CummeRbund (http://compbio.mit.edu/cummeRbund/), SeqMonk, and custom R scripts. Differentially expressed genes were identified by CummeRbund. […]

library_books

Maser: one stop platform for NGS big data from analysis to visualization

2018
PMCID: 5905357
PMID: 29688385
DOI: 10.1093/database/bay027

[…] s) and the analysis conducted.As a result, the Maser pipeline produces a report that summarizes the output of all the embedded tools (). For example, on the RNA-seq pipeline, ‘TopHat2, CuffLinks2 and CummeRbund + GE’ creates a report that contains the results of mapping by TopHat2, gene prediction and differential gene expression analysis by CuffLinks2, and visualization of CuffLinks2 outputs by c […]

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Gene duplicates cause hybrid lethality between sympatric species of Mimulus

2018
PLoS Genet
PMCID: 5896889
PMID: 29649209
DOI: 10.1371/journal.pgen.1007130
call_split See protocol

[…] fferential expression for all pairwise comparisons using default parameters for both program. For data management and sorting, we used Microsoft excel, the R statistical package [], and the R package CummeRbund []. Gene ontology (GO) enrichment analyses were carried out for particular subsets of data that exhibited patterns of differential expression between white and green seedlings. To perform t […]

Citations

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CummeRbund institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA

CummeRbund review

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Arup Ghosh

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Desktop
Cummerbund part of the tuxedo pipeline is a great R package, that takes cuffdiff output and has several features for further exploration of data including visualizations.