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OrderedList specifications

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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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No version available

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Publication for OrderedList

OrderedList citations

 (11)
library_books

Integrated omics dissection of proteome dynamics during cardiac remodeling

2018
Nat Commun
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 […]

library_books

Comprehensive transcriptional map of primate brain development

2016
Nature
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 […]

library_books

Increased Expression of Interferon Signaling Genes in the Bone Marrow Microenvironment of Myelodysplastic Syndromes

2015
PLoS One
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 […]

library_books

Mast cells are required for full expression of allergen/SEB induced skin inflammation

2013
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% […]

library_books

Clusterin regulates β amyloid toxicity via Dickkopf 1 driven induction of the wnt–PCP–JNK pathway

2012
Mol Psychiatry
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 […]

library_books

Computational Analysis of mRNA Expression Profiles Identifies MicroRNA 29a/c as Predictor of Colorectal Cancer Early Recurrence

2012
PLoS One
PMCID: 3278467
PMID: 22348113
DOI: 10.1371/journal.pone.0031587

[…] “target prediction database” for details). the detailed procedures were as follows: (1) mrna in each study subject was ranked by its expression level, and then scored according to its rank using the orderedlist method of bioconductor , and (2) the expression score of each microrna in each subject was imputed by calculating the difference between the mean of weighted rank scores of its target […]


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

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