AnnotationDbi statistics

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AnnotationDbi specifications

Information


Unique identifier OMICS_15773
Name AnnotationDbi
Alternative name Annotation Database Interface
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 1.42.1
Stability Stable
Requirements
methods, KEGG.db, IRanges, utils, BiocStyle, stats4, RUnit, S4Vectors(>=0.9.25), knitr, GO.db, org.Hs.eg.db, RSQLite, DBI, R(>=2.7.0), graph, reactome.db, EnsDb.Hsapiens.v75, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu95av2.db, org.Sc.sgd.db, AnnotationForge, BiocGenerics(>=0.23.1), Biobase(>=1.17.0), org.At.tair.db, hom.Hs.inp.db
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Hervé Pagès

AnnotationDbi citations

 (49)
library_books

Single cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis

2018
eLife
PMCID: 5860872
PMID: 29555020
DOI: 10.7554/eLife.29312.055

[…] The mRNA microarray data were analyzed using oligo, phylobase, methods, biobase, stats, ggplot2, gplots, matrixstats, graphics, annotationdbi and limma packages in R (). […]

library_books

Use of deep neural network ensembles to identify embryonic fetal transition markers: repression of COX7A1 in embryonic and cancer cells

2017
Oncotarget
PMCID: 5814259
PMID: 29487692
DOI: 10.18632/oncotarget.23748

[…] mall batches and then combined the data for analysis. After obtaining probe expression data, we converted it to gene expression using annotation tables, available from GEO for Illumina platforms and ‘AnnotationDbi’ package from Bioconductor for Affymetrix platforms. Such tables contain probe-gene mapping for particular microarray platform. If multiple probes were mapped to the same gene, we used g […]

library_books

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR

2017
F1000Res
PMCID: 5747346
PMID: 29333247
DOI: 10.5256/f1000research.14317.r28483

[…] el stats graphics grDevices utils datasets methods [9] base other attached packages: [1] org.Mm.eg.db_3.4.2 [2] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 [3] GenomicFeatures_1.30.0 [4] AnnotationDbi_1.40.0 [5] Biobase_2.38.0 [6] GenomicRanges_1.30.0 [7] GenomeInfoDb_1.14.0 [8] IRanges_2.12.0 [9] S4Vectors_0.16.0 [10] BiocGenerics_0.24.0 [11] edgeR_3.20.1 [12] limma_3.34.0 [13] […]

call_split

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

2017
Stem Cell Reports
PMCID: 5830993
PMID: 29056335
DOI: 10.1016/j.stemcr.2017.09.018
call_split See protocol

[…] he elimination algorithm as implemented in the topGO R package (version 2.12.0). Additional data and annotations were obtained from other Bioconductor R packages (org.Hs.eg.db [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 separately for enrichment at both ends of the […]

library_books

Multidimensional pooled shRNA screens in human THP 1 cells identify candidate modulators of macrophage polarization

2017
PLoS One
PMCID: 5570424
PMID: 28837623
DOI: 10.1371/journal.pone.0183679

[…] . For each comparison, differentially expressed genes were defined as those exhibiting an absolute FC ≥ 1.5 and p-value < 0.05. Annotation data for probes was obtained using the Bioconductor packages AnnotationDbi and hgu133plus2.db. […]

library_books

The atopic dermatitis blood signature is characterized by increases in inflammatory and cardiovascular risk proteins

2017
Sci Rep
PMCID: 5562859
PMID: 28821884
DOI: 10.1038/s41598-017-09207-z

[…] among groups was carried out using linear models for high-throughput data on R’s limma framework. Protein annotations, as well as Gene-Protein relationships were obtained by using UniPro IDs and R’s AnnotationDbi package. […]

Citations

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AnnotationDbi review

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Martin Abba

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Desktop
R/Bioconductor package that provide easy to use functions for gene annotation retrieved from data bases likes org.Hs.eg.db, etc.