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CAP-miRSeq specifications

Information


Unique identifier OMICS_04271
Name CAP-miRSeq
Alternative name Comprehensive Analysis Pipeline for microRNA Sequencing data
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Comprehensive Analysis Pipeline for microRNA Sequencing data

CAP-miRSeq citations

 (12)
library_books

Regulatory role of microRNA in mesenteric lymph nodes after Salmonella Typhimurium infection

2018
PMCID: 5796392
PMID: 29391047
DOI: 10.1186/s13567-018-0506-1

[…] Based on CAP-miRSeq analysis [], 110 differentially expressed (DE) miRNA were identified in porcine MLN after Salmonella Typhimurium infection. Amongst those, 50 were downregulated (fold change—FC—ranging from […]

library_books

Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries)

2018
BMC Genomics
PMCID: 5789708
PMID: 29378514
DOI: 10.1186/s12864-017-4400-4

[…] te. We observed that the most commonly detected miRNAs had the same or very similar coordinates, thus providing further verification of a true novel miRNA. We used this approach as implemented in the CAP-miRSEQ pipeline, and all novel miRNAs and their corresponding genome coordinates were listed in a table. All DEGs were used for GO annotations and KEGG pathway analyses. […]

library_books

The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome

2017
Genes
PMCID: 5664119
PMID: 29027980
DOI: 10.3390/genes8100269

[…] FDR is the expected fraction of false positive tests among significant tests and was calculated using the Benjamini-Hochberg multiple testing adjustment procedure. We set the FDR value (q ≤ 0.1).The Comprehensive Analysis Pipeline for microRNA sequencing data (CAP-miRSeq) was used for read pre-processing, alignment, mature/precursor/novel miRNA detection and quantification, and data visualization […]

call_split

Integrated transcriptomic and proteomic analysis of the molecular cargo of extracellular vesicles derived from porcine adipose tissue derived mesenchymal stem cells

2017
PLoS One
PMCID: 5363917
PMID: 28333993
DOI: 10.1371/journal.pone.0174303
call_split See protocol

[…] APRSeq v.1.2.1 system and the Bioinformatics Core standard tool, which includes alignment with TopHat 2.0.6 [, ] and gene counts with the featureCounts software []. miRNA-Seq data were analyzed using CAP-miRSeq v1.1 [] and normalization and differential expression analysis performed using edgeR 2.6.2 []. Gene expression was normalized to 1 million reads and corrected for gene length (reads per kil […]

call_split

Aging and serum exomiR content in women effects of estrogenic hormone replacement therapy

2017
Sci Rep
PMCID: 5307383
PMID: 28195143
DOI: 10.1038/srep42702
call_split See protocol

[…] n 18 was used for retrieving miR information. Differential expression analysis was performed on miRDeep2 output data utilizing a custom R script adapted from the differential expression module in the CAP-miRSEQ tool. The tools employed in different steps rely on various programming languages. To simplify the workflow a set of R functions was created to carry out QC, trimming, miRDeep analysis and […]

library_books

miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep sequencing data analysis

2017
Brief Bioinform
PMCID: 5952930
PMID: 28073746
DOI: 10.1093/bib/bbw140

[…] /sbbi.unl.edu/miRDis/supp/s1.docx). For instances, in human break milk data, most of other tools detected too many or too few miRNAs (e.g. 737–920 or 35 in average among 20 samples), while miRDis and CAP-miRSeq detected ∼500 sequences, which is reasonably close to the current report of ∼300 miRNAs confirmed in breast milk cell through microarray and polymerase chain reaction [, ]. It is notable th […]

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CAP-miRSeq institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Chinahester, MN, USA

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