CODOC statistics

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Citations per year

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

This map represents all the scientific publications referring to CODOC per scientific context
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Associated diseases

This word cloud represents CODOC usage per disease context
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Protocols

CODOC specifications

Information


Unique identifier OMICS_04175
Name CODOC
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format BAM
Operating system Unix/Linux
Programming languages Java, R
Computer skills Advanced
Version 0.0.2
Stability Stable
Maintained Yes

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Publication for CODOC

CODOC citations

 (2)
call_split

The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation

2015
PLoS Pathog
PMCID: 4570706
PMID: 26371761
DOI: 10.1371/journal.ppat.1005160
call_split See protocol

[…] ion increase or decrease). We also extracted strand-specific, normalized depth-of-coverage signals (i.e., the counts of reads overlapping a particular genomic position) from the read alignments using CODOC [] and converted them to the BigWig data format to enable manual inspection in a genome browser. […]

call_split

Germline recessive mutations in PI4KA are associated with perisylvian polymicrogyria, cerebellar hypoplasia and arthrogryposis

2015
Hum Mol Genet
PMCID: 4459391
PMID: 25855803
DOI: 10.1093/hmg/ddv117
call_split See protocol

[…] ). Variants were called with Platypus version 0.5.2 () (www.well.ox.ac.uk/platypus) with default settings except for minFlank = 0. Coverage was calculated on deduplicated BAM files using bedtools and CODOC (). Variant calling was performed across all five BAM files simultaneously, producing a multi-sample VCF. The WES data from the family were extensively examined in Ingenuity Variant Analysis (ve […]


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CODOC institution(s)
Center for Integrative Bioinformatics Vienna (CIBIV), Max F Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
CODOC funding source(s)
Supported by the CIBIV household budget.

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