zFPKM protocols

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zFPKM specifications

Information


Unique identifier OMICS_20121
Name zFPKM
Alternative name NFPKM
Software type Application/Script
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 1.3.0
Stability Stable
Requirements
limma, GEOquery, SummarizedExperiment, edgeR, dplyr, ggplot2, knitr, stringr, tidyr, R(>=3.4.0), checkmate, printr
Maintained Yes

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Maintainers


  • person_outline Traver Hart <>
  • person_outline Ron Ammar <>

Additional information


Manual: http://bioconductor.org/packages/devel/bioc/manuals/zFPKM/man/zFPKM.pdf

Publication for zFPKM

zFPKM in pipelines

 (4)
2017
PMCID: 5427898
PMID: 28273906
DOI: 10.1038/s41598-017-00176-x

[…] enrichment for a genomic region. rna-seq reads were aligned to the mouse genome assembly mm9 by tophat. gene expression levels (fpkm) were computed by cufflinks. genes were considered expressed by zfpkm > −3., a sequencing library was prepared from genomic dna of wild type c2c12 cells and sequenced using illumina’s hiseq 2000 system. all 76 bp single-end reads were mapped onto the mouse […]

2016
PMCID: 4879514
PMID: 26928872
DOI: 10.1111/mec.13596

[…] enrichment of gene ontology terms were performed with the r bioconductor package goseq (young et al. ). significant go terms were bonferroni corrected for multiple testing. r scripts for calculating zfpkm, p st and τ are available online at https://github.com/severinevo/gene_expression., data for the number of protein–protein interactions of chicken genes were obtained from the funcoup v. 3.0 […]

2015
PMCID: 4468903
PMID: 26040272
DOI: 10.1038/ncomms8330

[…] cufflinks were used to map rna-seq data to final nrw gene annotations and estimate transcript abundance. cufflinks-derived fpkm values were extracted using in-house scripts and further normalized to zfpkm using the approach by hart et al.. statistical analyses of gene expression patterns were performed using r v3.1.1. expression breadth (τ) was estimated according to yanini et al.. p values […]

2015
PMCID: 4576709
PMID: 26108680
DOI: 10.1093/molbev/msv147

[…] per million mapped fragments) normalized gene expression values and normalized further using the method of , a between-sample normalization method of log2 fpkm values similar to a z-transformation (zfpkm). we applied an expression cutoff of 0.125 zfpkm as suggested in that study., m:f ratios were calculated for genes with data available for all five males and all five females; inclusion […]

zFPKM in publications

 (6)
PMCID: 5683568
PMID: 29131848
DOI: 10.1371/journal.pone.0185612

[…] differentially expressed between two organs[]., to minimize influence of the transcript level on estimation of differentiation of the m6a extent, m6a-seq data was normalized by a specific algorithm, nfpkm (nfpkm = mfpkm in m6a-seq/log (fpkm in rna-seq, 2)). χ2 tests were also used to estimate whether nfpkm of a m6a modified transcript was significantly different between two organs using r 3.1. […]

PMCID: 5630512
PMID: 28920956
DOI: 10.1038/nm.4406

[…] 6.0 for mac (graphpad software, la jolla california usa, www.graphpad.com)., actively expressed genes for excitatory and inhibitory neurons were determined by calculating the normalized fpkm (zfpkm) and using zfpkm ≥ 3 for the active gene cutoff as previously described., statistical analyses were performed using graphpad prism version 6.0 for mac (graphpad software, la jolla california […]

PMCID: 4879514
PMID: 26928872
DOI: 10.1111/mec.13596

[…] cufflinks v. 2.1.1 (trapnell et al. ). fpkm values were then further normalized using the procedure described in hart et al. (), and genes were defined as being expressed using the cut‐off of 0.125 zfpkm suggested in that study. we also extracted raw read counts from these mappings for analyses of differential expression in edger., we calculated euclidean distances from zfpkm expression values […]

PMCID: 4714525
PMID: 26667818
DOI: 10.1186/s13059-015-0839-2

[…] minimize effect of gene transcript level on estimation of m6a methylation extent of the transcripts and to more precisely evaluate differential m6a methylation among organs, we applied an algorithm ‘nfpkm’ to each transcript to estimate differential m6a methylation among three organs (see details in the section of this paper). two fold change and chi-square were applied for estimation […]

PMCID: 4619268
PMID: 26493315
DOI: 10.1186/s12864-015-2088-x

[…] relative quantization experiments. the normalized expression values (rn) of the selected transcripts of p. perniciosus in males and females were compared to the respective normalized fpkm values (nfpkm), resulting in statistically significant positive correlation. in particular, the pearson correlation coefficient r was 0.743 in males (p = 0.014) and 0.862 in females (p = 0.001), showing […]

zFPKM institution(s)
Donnelly Centre, Banting & Best Department of Medical Research, University of Toronto, Toronto, ON, Canada; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
zFPKM funding source(s)
Supported by NIH grants U19 AI063603, U01 AI084146 and U01 AI063594 (ARRA); by National Institutes of Health TL1 RR025772–03.

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