NOISeq specifications

Information


Unique identifier OMICS_01311
Name NOISeq
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
Stability Stable
Requirements methods, Biobase, splines, Matrix
Maintained Yes

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Documentation


Maintainer


  • person_outline Sonia Tarazona <>

NOISeq article

NOISeq citations

 (8)
2018
PMCID: 5940186

[…] normalized to ercc spike-in values across samples using bioconductor package ruvseq_1.8.0 [40]. we removed non-expressed genes by requiring more than 5 reads for each gene. r bioconductor package noiseq was used evaluate and access the quality control of the count data [41]., paired student’s t tests were used to calculate p-values when comparing methods for exosomal rna extraction. one-way […]

2018
PMCID: 5827294

[…] sum of squares of deviations was used to calculate the distance between samples. the samples for both shoots and roots in standard, salt stress and recovery conditions were clustered respectively. noiseq method was used to screen differentially expressed genes between three biological samples using the criteria: |log2ratio| ≥ 1 and probability ≥ 0.8 (tarazona et al., 2011). for gene expression […]

2017
PMCID: 5645375

[…] approximately 34.6 in wt and 34.9 million reads in tg(fabp10:nras 61k) transgenic zebrafish belonged to the zebrafish genome by analysis as described by bowtie 24 along with enrichment analysis with noiseq.25. 661 down-regulated- and 1214 up-regulated- differentially expressed genes in tg(fabp10:nras 61k) transgenic zebrafish were observed (fig. 4a and supplementary table 1). functions […]

2017
PMCID: 5395571

[…] previously (sun et al., 2015a). prediction of tfs was performed by using the hmmsearch program. identification of differentially expressed genes (degs) between samples was performed with r package ‘noiseq’ (tarazona et al., 2011). a threshold of fold-change ≥ 2 and divergence probability ≥ 0.8 was used for filtering the significance of the gene expression difference. heatmap visualizations […]

2016
PMCID: 5112795

[…] expressions of different mrna transcripts were also calculated. gatk was used to detect the snps in the genome, and snps that were supported by less than four reads were filtered out., in the study, noiseq software package [22]was selected to screen for degs. firstly, the background noise was calculated for every two groups. using the obtained fpkm values, the averaged expression value of genes […]

NOISeq institution(s)
Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain; Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia,Valencia, Spain
NOISeq funding source(s)
European Union Seventh Framework Programme [FP7/2007-2013, 306000]; Spanish Ministry of Science and Innovation [MICINN, BIO2008-04638-E], in the framework of ERA-Net Pathogenomics; MICINN [DPI2008-06880-C03-03/DPI]

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