NOISeq protocols

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 <>

Publication for NOISeq

NOISeq IN pipelines

 (25)
2018
PMCID: 5786550
PMID: 29403517
DOI: 10.3389/fpls.2018.00007

[…] of degs were performed as described in a previous study (sui et al., 2015). the degs with a fold change of ≥2 and divergence probability ≥0.8 between different samples were identified using the noiseq method (tarazona et al., 2011)., quantitative real-time rt-pcr (qrt-pcr) analysis was performed to validate the rna-seq results. twelve degs were randomly selected for qrt-pcr. all primers […]

2018
PMCID: 5789709
PMID: 29378633
DOI: 10.1186/s40168-018-0404-9

[…] ile 2: figure s1b), and the majority mapped to protein coding rna (additional file 2: figure s1c) with sufficient coverage (additional file 2: figure s1d). gene counts were filtered and normalized in noiseq [29, 30], yielding a total of 15,448 features for analysis (additional file 3: dataset s1). arsynseq [31] was used to control for batch effects associated with different sequencing runs (additi […]

2018
PMCID: 5789820
PMID: 29382956
DOI: 10.1038/s41598-018-20308-1

[…] read counts were summed for each unique geneid and normalized by total mapped read counts. statistical analysis for detection of differentially expressed genes was done using noiseqbio from the noiseq package34, with threshold of pnoi = 0.95, corresponding to false discovery rate adjusted p-values of 0.05. kegg pathway analysis35 was performed by mapping the kegg annotated differentially […]

2018
PMCID: 5827294
PMID: 29520289
DOI: 10.3389/fpls.2018.00217

[…] 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 […]

2018
PMCID: 5833345
PMID: 29352142
DOI: 10.1038/s41419-017-0066-8

[…] clean reads were then obtained and stored as fastq format. hisat45 was used to map clean reads to the genome of hg19. gene expression levels are quantified by a software package called rsem46. noiseq method47 was used to screen differentially expressed genes between two groups., dlbcl cells were chemically cross-linked with 1% formaldehyde solution for 10 min at room temperature […]

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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