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Protocols

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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Versioning


No version available

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 citations

 (8)
library_books

High throughput m6A seq reveals RNA m6A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana

2017
PLoS One
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. […]

library_books

Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome

2017
Nat Med
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 […]

call_split

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina associated Genes

2017
Sci Rep
PMCID: 5427898
PMID: 28273906
DOI: 10.1038/s41598-017-00176-x
call_split See protocol

[…] 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 […]

library_books

Divergence in gene expression within and between two closely related flycatcher species

2016
Mol Ecol
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 […]

library_books

Transcriptome wide high throughput deep m6A seq reveals unique differential m6A methylation patterns between three organs in Arabidopsis thaliana

2015
Genome Biol
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 […]

library_books

De novo assembly and sex specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

2015
BMC Genomics
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 […]


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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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