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RNASeqPower specifications

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Unique identifier OMICS_15095
Name RNASeqPower
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 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Maintained Yes

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Publication for RNASeqPower

RNASeqPower citations

 (9)
library_books

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis

2018
MBio
PMCID: 5904416
PMID: 29666288
DOI: 10.1128/mBio.00575-18

[…] ample. The statistical power of our study, and thus the likelihood of identifying a true positive, was found to be 0.8 when the effect size was set at 2.75-fold cutoff, calculated using the R program RNASeqPower (v3.5) () within the Bioconductor package using a sample size of 3, a false-discovery rate of 0.05, and the lowest sequencing depth in all libraries (determined through SAMtools mpileup). […]

library_books

MiRNA profiling of gastrointestinal stromal tumors by next generation sequencing

2017
Oncotarget
PMCID: 5514905
PMID: 28402935
DOI: 10.18632/oncotarget.16664

[…] ntially expressed miRNAs with a corrected p-value < 1 × 10−10 and an absolute log2 fold change > 3.5 were selected for validation analysis. The statistical power of the study was calculated using the RNASeqPower package []. The small RNA-seq data have been deposited in NCBI's Gene Expression Omnibus [] and are accessible through GEO Series accession number GSE89051 (https://www.ncbi.nlm.nih.gov/ge […]

library_books

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer

2016
Oncogene
PMCID: 5245767
PMID: 27748765
DOI: 10.1038/onc.2016.382

[…] sion in MCF7 cells, but would be expected to show limited estrogen stimulation of indirect targets. For each condition, three independent replicate samples were analysed by RNA-seq. Analysis with the RNASeqPower package in R for our data showed that three replicates gave a power >0.8 for a fold change of 1.5. As the sequencing data for one of the three replicates for MCF7-Y537S cells treated with […]

library_books

Using Synthetic Mouse Spike In Transcripts to Evaluate RNA Seq Analysis Tools

2016
PLoS One
PMCID: 4839710
PMID: 27100792
DOI: 10.1371/journal.pone.0153782

[…] M matrix. Quantification results of HTSeq and RSEM were further normalized by using CQN []. ROC curves were calculated using pROC package []. Power analysis was performed with Scotty [] and R package RNASeqPower [].The spike-ins plots were done using Matlab, Partek and R. For spike-ins quantification plots an offset of 10e-3 was added to FPKM values before log2 transformation.EBSeq [] was used to […]

library_books

RNA sequencing reveals region specific molecular mechanisms associated with epileptogenesis in a model of classical hippocampal sclerosis

2016
Sci Rep
PMCID: 4776103
PMID: 26935982
DOI: 10.1038/srep22416

[…] ressed genes with p < 0.05 (after correction for multiple tests) was generated. The EdgeR package was used to calculate the Biological coefficient of variance of the present data (BV = 0161), and the RNASeqPower package was used to calculate the statistical power of the present experiment, considering the number of biological replicates used. A power greater than 0.9 was found for genes that prese […]

call_split

Transcriptome Sequencing (RNAseq) Enables Utilization of Formalin Fixed, Paraffin Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development

2016
PLoS One
PMCID: 4764764
PMID: 26901863
DOI: 10.1371/journal.pone.0149743
call_split See protocol

[…] tumors vs. normals). This sample size is sufficient to achieve a power of 0.85, where we apply a standard deviation of 0.7 of the expressed genes, an effect size of 2, and an alpha of 0.05 (R package RNASeqPower in https://www.bioconductor.org).Assembly of reads and alignment of the contigs to the Human genome assembly GRCh38 was guided by Tophat and Bowtie. An empirical expression filter was appl […]


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RNASeqPower institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Chinahester, MN, USA; Mayo Vaccine Research Group, Mayo Clinic, Chinahester, MN, USA; Program in Translational Immunovirology and Biodefense, Mayo Clinic, Chinahester, MN, USA
RNASeqPower funding source(s)
This work was funded through the Center for Individualized Medicine at Mayo Clinic (112222) and federal funds from the National Institute of Health, under contract number U01 AI089859.

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