mirData: Example of IsomirDataSeq with human brain miRNA counts data
In isomiRs: Analyze isomiRs and miRNAs from small RNA-seq
Description
Usage
Format
Author(s)
Source
References
Description
This data set is the object return by IsomirDataSeqFromFiles.
It contains miRNA count data from 14 samples: 7 control individuals (pc) and
7 patients with Parkinson's disease in early stage (Pantano et al, 2016).
Use colData to see the experiment design.
Usage
1
data("mirData")
Format
a IsomirDataSeq class.
Author(s)
Lorena Pantano, 2018-04-27
Source
Data is available from GEO dataset under accession number GSE97285
Every sample was analyzed with seqbuster tool, see
http://seqcluster.readthedocs.org/mirna_annotation.html for
more details. You can get same files running the small RNA-seq
pipeline from https://github.com/bcbio/bcbio-nextgen.
bcbio_nextgen was used for the full analysis.
See raw-data.R to know how to recreate the object.
This script is inside "extra" folder of the package.
References
Pantano L, Friedlander MR, Escaramis G, Lizano E et al.
Specific small-RNA signatures in the amygdala at premotor and motor stages
of Parkinson's disease revealed by deep sequencing analysis.
Bioinformatics 2016 Mar 1;32(5):673-81. PMID: 26530722
isomiRs documentation built on Jan. 31, 2021, 2 a.m.
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Description Usage Format Author(s) Source References
Description
This data set is the object return by IsomirDataSeqFromFiles.
It contains miRNA count data from 14 samples: 7 control individuals (pc) and
7 patients with Parkinson's disease in early stage (Pantano et al, 2016).
Use colData to see the experiment design.
Usage
1 | data("mirData")
|
Format
a IsomirDataSeq class.
Author(s)
Lorena Pantano, 2018-04-27
Source
Data is available from GEO dataset under accession number GSE97285
Every sample was analyzed with seqbuster tool, see http://seqcluster.readthedocs.org/mirna_annotation.html for more details. You can get same files running the small RNA-seq pipeline from https://github.com/bcbio/bcbio-nextgen.
bcbio_nextgen was used for the full analysis.
See raw-data.R to know how to recreate the object.
This script is inside "extra" folder of the package.
References
Pantano L, Friedlander MR, Escaramis G, Lizano E et al. Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Bioinformatics 2016 Mar 1;32(5):673-81. PMID: 26530722
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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