Annmap statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Annmap
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Tool usage distribution map

This map represents all the scientific publications referring to Annmap per scientific context
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Protocols

Annmap specifications

Information


Unique identifier OMICS_00900
Name Annmap
Interface Web user interface
Restrictions to use None
Biological technology Affymetrix
Computer skills Basic
Stability No
Maintained No

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Publications for Annmap

Annmap citations

 (11)
library_books

24h gene variation effect of combined bevacizumab/erlotinib in advanced non squamous non small cell lung cancer using exon array blood profiling

2017
J Transl Med
PMCID: 5372268
PMID: 28359318
DOI: 10.1186/s12967-017-1174-z

[…] , 439,778 exonic probe sets (within 38,900 genes) were kept in the analysis, after filtering out intronic, intergenic and unreliable probe sets (according to the nomenclature defined in the R package annmap []). Raw data (Affymetrix CEL files) have been deposited in NCBI’s Gene Expression Omnibus (GEO), and are accessible through GEO Series accession number GSE61676. The exon level probe sets were […]

call_split

Hypoxia driven splicing into noncoding isoforms regulates the DNA damage response

2016
PMCID: 5417364
PMID: 28480052
DOI: 10.1038/npjgenmed.2016.20
call_split See protocol

[…] and supplied to edgeR to call differential expression (absolute fold-change >2 relative to 0 h; false discovery rate (FDR) <1%) at each time point. Annotation was supplied by the Bioconductor package annmap. […]

library_books

SOX7 enforced expression promotes the expansion of adult blood progenitors and blocks B cell development

2016
Open Biol
PMCID: 4967825
PMID: 27411892
DOI: 10.1098/rsob.160070

[…] se array remained for differential gene expression analysis. Annotations and cross-mappings between probesets, exons and genes were obtained from Ensembl mouse genome using the R/BioConductor package Annmap (BioConductor 2.14). […]

library_books

Evaluation and validation of a robust single cell RNA amplification protocol through transcriptional profiling of enriched lung cancer initiating cells

2014
BMC Genomics
PMCID: 4320548
PMID: 25519510
DOI: 10.1186/1471-2164-15-1129

[…] alue calculated by panp was less than 0.05. For each replicate, the present probesets were mapped to the genes using the ENSEMBL human gene annotation database version 70 via the BioConductor package annmap []. Gene lists for one sample were compiled from the two replicates, containing the genes which were present in both replicates.Data for the MCF7 and MCF10A samples were generated using Affymet […]

call_split

Epithelial and Stromal MicroRNA Signatures of Columnar Cell Hyperplasia Linking Let 7c to Precancerous and Cancerous Breast Cancer Cell Proliferation

2014
PLoS One
PMCID: 4133372
PMID: 25122196
DOI: 10.1371/journal.pone.0105099
call_split See protocol

[…] uctor and Ingenuity Systems (Redwood City, CA). The RMA was used to normalise and summarise the expression values at the probeset level . Probesets were mapped to genes using the Bioconductor package annmap to position probesets relative to Ensembl version 60 annotations . The R package Limma was used to find differentially expressed genes and Ingenuity to find the enriched pathways from the diff […]

library_books

A global non coding RNA system modulates fission yeast protein levels in response to stress

2014
Nat Commun
PMCID: 4050258
PMID: 24853205
DOI: 10.1038/ncomms4947

[…] yield an extensive transcription map of S. pombe. These regions were then positioned relative to known annotation and labelled according to the gene(s) they overlapped, using the Bioconductor package annmap. Next, we identified for each transcribed locus its 5′- and 3′-extent in a given sample. Subsequent analysis was performed in R and Bioconductor software unless otherwise stated. […]


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Annmap institution(s)
Cancer Research UK, Bioinformatics Group, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Withington, Manchester, UK

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