Glimma statistics

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Popular tool citations

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Associated diseases

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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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Maintainers


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

Publication for Glimma

Glimma in pipelines

 (2)
2016
PMCID: 4937821
PMID: 27441086
DOI: 10.5256/f1000research.9688.r14436

[…] block could it be moved below., figs 5-8 have bold headings but figs 1-4 don't is that an error., could perhaps modify title to reflect the order in which the tools are used - edger, limma & glimma., it would be nice for consistency if the colours in the glimma interactive mds plots matched the colours used in the static mds plots in fig 3., i have read this submission. i believe […]

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

[…] choices they make (e.g., filtering out unexpressed genes, specifying model coefficients, etc) at a more accessible level., while both edger and limma are well known, popular bioconductor packages, glimma is a new package that was released in april 2016. this package uses the d3.js javascript library to generate interactive html documents that can be viewed locally, rather than needing […]


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Glimma in publications

 (3)
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 […]

PMCID: 5264264
PMID: 28123349
DOI: 10.7150/ijbs.17390

[…] 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 […]

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

[…] 2; referees: 3 approved], cwl and mer developed the workflow and wrote the article with input from ma (gene set testing), ss (glimma) and gks (general editing and advice on direction of the article)., competing interests: the authors declare that they have no competing interests., the ability to easily and efficiently […]


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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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