fdrtool protocols

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fdrtool specifications

Information


Unique identifier OMICS_17556
Name fdrtool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.15
Stability Stable
Requirements
stats, graphics, grDevices, R(≥3.0.2)
Source code URL https://cran.r-project.org/src/contrib/fdrtool_1.2.15.tar.gz
Maintained Yes

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Maintainers


  • person_outline Korbinian Strimmer <>
  • person_outline Korbinian Strimmer <>

Publication for fdrtool

fdrtool in pipeline

2018
PMCID: 5755028
PMID: 29301589
DOI: 10.1186/s13073-017-0511-4

[…] in r (version 3.0.1) with several analysis packages (stringr, version 0.6.2; biostrings, version 2.28.0; rsamtools, version 1.12.4; bsgenome. hsapiens. ucsc.hg19, version 1.3.19; plyr, version 1.8, fdrtool, version1.2.11). the raw fastq files from the sequencing were deposited at ncbi sequence read archive (sra) with bioproject accession number prjna419878., the genes with significant […]


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fdrtool in publications

 (124)
PMCID: 5940833
PMID: 29740045
DOI: 10.1038/s41598-018-25515-4

[…] 3.0 software. significantly altered genes were defined by fc > 1.3, p-value < 0.05 and fdr < 0.10. false-discovery rates for metabolite and gene expression profiling were estimated using fdrtool in r. exosome marker levels were compared between groups using the mann whitney u-test in prism (p < 0.05)., all data generated or analyzed during this study are included in this published […]

PMCID: 5934379
PMID: 29725116
DOI: 10.1038/s41598-018-25163-8

[…] colleagues [tx-perco] was re-analysed with respect to correlation of transcripts to twelve months post-transplant egfr values. p-values of the correlation analysis were corrected with the r package fdrtool, setting the false discovery rate to <5%. all transcripts were mapped to their respective genes using the ensembl gene id as common denominator. all datasets used in the integrative […]

PMCID: 5891602
PMID: 29666629
DOI: 10.3389/fpls.2018.00419

[…] separately for each seed lot, again using the r package genabel. significance thresholds were defined by calculation of false discovery rates based on p-value statistics with the r package fdrtool (). for mgt, seed ea, and gsl content, cutoff values between -log10(p-value) = 0.73 and 2.046 were calculated. consequently, for all traits, only associations were taken into account […]

PMCID: 5799309
PMID: 29402907
DOI: 10.1038/s41598-018-19736-w

[…] was carried out on complex abiotic and biotic stresses, viz. salinity, cold, drought, fungal and insect, in rice. moreover, for the computation of fdr for each selected gene set, we executed the fdrtool function implemented in fdrtool r package which is based on the approach developed by strimmer (2008). the operational procedure of the gsaq approach and its implemented algorithm are shown […]

PMCID: 5880102
PMID: 29363612
DOI: 10.1074/mcp.RA117.000189

[…] for differential protein expression, each patient-sample was treated individually. protein ratios were calculated for all the protein groups quantified with at least 2 peptides. the r-package “fdrtool” () was used to fit a two components model on the median centered log2 ratio distributions using the statistic 'normal' (supplemental figs. s2, s6, and s10). protein groups with a ratio […]


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fdrtool institution(s)
Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany

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