Glimma statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Glimma
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Tool usage distribution map

This map represents all the scientific publications referring to Glimma per scientific context
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Associated diseases

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Popular tool citations

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Protocols

Glimma specifications

Information


Unique identifier OMICS_16101
Name Glimma
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some outputs from limma, edgeR or DESeq2.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.8.2
Stability Stable
Requirements
limma, methods, stats, IRanges, GenomicRanges, utils, testthat, S4Vectors, BiocStyle, grDevices, SummarizedExperiment, edgeR, DESeq2, rmarkdown, knitr, R(>=3.4.0), pryr, jsonlite
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Matthew Ritchie
  • person_outline Shian Su
  • person_outline Charity Law

Publication for Glimma

Glimma citations

 (4)
library_books

Easy and efficient ensemble gene set testing with EGSEA

2017
F1000Res
PMCID: 5747338
PMID: 29333246
DOI: 10.5256/f1000research.13583.r27972

[…] RNA-seq analysis follows on directly from the workflow of Law et al. (2016) which performs a differential gene expression analysis on this data set using the Bioconductor packages edgeR , limma and Glimma with gene annotation from the Mus.musculus package . The limma package offers a well-developed suite of statistical methods for dealing with differential expression for both microarray and RNA […]

library_books

Glimma: interactive graphics for gene expression analysis

2017
Bioinformatics
PMCID: 5870845
PMID: 28203714
DOI: 10.1093/bioinformatics/btx094

[…] aphics are ongoing and to date very few Bioconductor packages enable effective interactive exploration of data. To solve this problem for the common task of gene expression analysis, we developed the Glimma package which adds interactivity to two popular data displays. […]

call_split

Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation

2017
PMCID: 5264264
PMID: 28123349
DOI: 10.7150/ijbs.17390
call_split See protocol

[…] r the conditions 96-hour and 40-hour were obtained from the supplementary data provided for GSE69461. The RPKM values from all the samples were further subjected to statistical analysis using limma , Glimma (http://bioconductor.org/packages/release/bioc/html/Glimma.html) and edgeR - Bioconductor packages. The statistically significant genes among different samples were obtained based on the fold c […]

library_books

RNA seq analysis is easy as 1 2 3 with limma, Glimma and edgeR

2016
F1000Res
PMCID: 4937821
PMID: 27441086
DOI: 10.5256/f1000research.9688.r14436

[…] es can be generated using the plotMD function, with the differentially expressed genes highlighted. plotMD (tfit, column = 1 , status =dt[, 1 ], main = colnames (tfit)[ 1 ], xlim = c ( - 8 , 13 )) Glimma extends this functionality by providing an interactive mean-difference plot via the glMDPlot function. The output of this function is an html page, with summarised results in the left panel (si […]


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Glimma institution(s)
Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia; ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
Glimma funding source(s)
Supported by the National Health and Medical Research Council (Project grants 1050661, 1045936, 1079756 and 1059622, Fellowships 1104924 and 1110206), a Viertel Fellowship, Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS.

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