OrderedList protocols

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OrderedList specifications

Information


Unique identifier OMICS_03525
Name OrderedList
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.52.0
Stability Stable
Requirements
methods, stats, graphics, Biobase, R(>=2.1.0), Biobase(>=1.5.12), twilight(>=1.9.2), twilight
Maintained Yes

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Publication for OrderedList

OrderedList in pipeline

2011
PMCID: 3120887
PMID: 21731767
DOI: 10.1371/journal.pone.0021495

[…] those mirnas in each brain region with ≥2 replicates detected as present for further analyses., comparison of the mirna expression levels measured by mirna-seq and microarray was performed with the orderedlist package implemented in r/bioconductor. for this test, we ranked mirnas from mirna-seq and microarray data separately based on their expression levels in fcx and in hp (normalized count […]


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OrderedList in publications

 (11)
PMCID: 5760723
PMID: 29317621
DOI: 10.1038/s41467-017-02467-3

[…] stouffer’s z score test. significance of correlation was reported as asymptotic p of spearman’s ρ. the similarity of gene lists in the meta-analysis of multi-omics data sets was compared using the orderedlist package (v.2.4) in r/bioconductor. significance of functional enrichment was reported as hypergeometric test p with benjamini–hochberg adjustment. the significance of protein–protein […]

PMCID: 5325728
PMID: 27409810
DOI: 10.1038/nature18637

[…] (419 * 418 = 175,142 comparisons). for each gene list comparison, we found the number of overlapping genes and calculated an overlap similarity score based on the weighted rank order of the lists (“orderedlist” package in r). we then generated a null distribution of similarity scores by shuffling gene lists 10 million times and calculated p values for observed similarity scores. we found […]

PMCID: 4372597
PMID: 25803272
DOI: 10.1371/journal.pone.0120602

[…] was created in cytoscape [] and its multicolorednodes plug-in []. the overall similarity of differential expression signatures between rcmd vs. control and raeb vs. control was assessed using the orderedlist r package [], which does not rely on a simple overlap of degs but instead considers the complete ordering of all genes in the two differential expression signatures to assess […]

PMCID: 3830701
PMID: 23752044
DOI: 10.1038/jid.2013.250

[…] the changes in expression of genes in human ad versus healthy skin from ad patients or healthy subjects were compared with those of orthologous genes in mouse eczematous versus healthy skin, using orderedlist algorithm (; ). this analysis detected significant similarity in gene expression in the skin between human ad and mouse ad-like dermatitis ( and ). the top genes contributing to 95% […]

PMCID: 3873038
PMID: 23164821
DOI: 10.1038/mp.2012.163

[…] were common to both. a test for similarities in ordered gene lists was then performed on the two lists using the orderedlists software package (http://www.bioconductor.org/packages/release/bioc/html/orderedlist.html) within the bioconductor r environment. a test of the significance of their ordering by fold change was performed, and in the top 500 genes a p-value of ≤0.000 was obtained (this […]


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OrderedList institution(s)
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany

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