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Protocols specifications


Unique identifier OMICS_16311
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 3.6.0
Stability Stable
AnnotationDbi, methods, RUnit, annotate, DBI, R(>=2.7.0), AnnotationDbi(>=1.41.4)
Maintained Yes




No version available



  • person_outline Marc Carlson citations


Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma

Sci Rep
PMCID: 5882888
PMID: 29615643
DOI: 10.1038/s41598-018-23609-7
call_split See protocol

[…] package in R. justRMA is an automated tool that both performs normalization using the Robust Multi-Array Average method and also automatically annotates all probes in the normalized dataset using the annotation database package. Normalization was performed on the full dataset and the NF2-associated schwannomas, as above. Mirroring the GEO2R analysis, each normalized dataset was analyz […]


Single cell RNA seq of rheumatoid arthritis synovial tissue using low cost microfluidic instrumentation

Nat Commun
PMCID: 5824814
PMID: 29476078
DOI: 10.1038/s41467-017-02659-x
call_split See protocol

[…] from the scde package on the scaled and normalized scRNA-seq data from each subset separately for the RABP3 patient. We used the genome wide annotation for humans as our reference (Carlson M (2017). Genome wide annotation for Human. R package version 3.4.1). We performed a PCA analysis and the top principle component for each gene set was obtained using the pagoda.pathway.wPCA funct […]


Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies

PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] NSG[0-9]+)\\.[0-9]+","\\1", rownames(rse))) gobp_enrichment <- enrichGO(prioritised_hits_ensembl_ids, universe = all_genes_ensembl_ids, OrgDb =, keyType = "ENSEMBL", ont = "BP", pAdjustMethod = "BH", pvalueCutoff = 0.05 […]


Parental micronutrient deficiency distorts liver DNA methylation and expression of lipid genes associated with a fatty liver like phenotype in offspring

Sci Rep
PMCID: 5812986
PMID: 29445184
DOI: 10.1038/s41598-018-21211-5
call_split See protocol

[…] orthologues (exported from Ensembl biomart) as input to DAVID, and the full set of identified orthologues was used as background. Genes belonging to specific GO annotations were identified using the Bioconductor (version 3.2.3) package, and mapped back to zebrafish orthologues. Colors in all heatmaps indicate row-normalized log FPKM values. The probability of observing a given number […]


Identification of human age associated gene co expressions in functional modules using liquid association

PMCID: 5787419
PMID: 29416677
DOI: 10.18632/oncotarget.23148

[…] bial (nerve), skin sun exposed lower leg (skin), thyroid, and whole blood respectively. We considered these nine tissues in our study. We also obtained the GO terms and KEGG pathways using R package ‘’ and ‘KEGG.db’ (on June 13, 2016). To avoid too general functions, we only used GO terms and KEGG pathways with less than 500 genes, resulting in 12199 GO terms and 279 KEGG pathways.It w […]


Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos

Stem Cell Reports
PMCID: 5830993
PMID: 29056335
DOI: 10.1016/j.stemcr.2017.09.018
call_split See protocol

[…] isher's exact test was applied with the elimination algorithm as implemented in the topGO R package (version 2.12.0). Additional data and annotations were obtained from other Bioconductor R packages ( [2.9.0], GO.db [2.9.0], AnnotationDbi [1.22.6]).Gene-level PCA projected loadings were used to test for GO gene set enrichment employing one-sided Wilcoxon rank-sum tests to test separate […]

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