GFOLD pipeline

GFOLD specifications

Information


Unique identifier OMICS_07340
Name GFOLD
Alternative name Generalized fold change
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Generalized fold change

GFOLD IN pipelines

 (7)
2018
PMCID: 5861405
PMID: 29361176
DOI: 10.1093/nar/gky008

[…] system (illumina). paired-end reads were aligned to the ucsc hg19 human reference genome using the hisat2 alignment program (42). ranked lists of differentially expressed genes were generated using gfold (43). for kegg pathway analysis, ranked lists with a log fold change either >0.5 or <0.5 were submitted to the david (database for annotation, visualization and integrated discovery […]

2017
PMCID: 5591532
PMID: 28886694
DOI: 10.1186/s12864-017-4077-8

[…] calculated as the reads mapped to reference genes or exons. the fpkm (fragments per kb per million of the mapped reads) parameter was employed to count the transcript data [77], whilst the algorithm gfold (generalized fold change) was adopted to produce biological meaning and the rankings of degs [78]. as the recurrent parent of mbi9915 and mbi9749, ccri36 was used to compare the two cssls […]

2017
PMCID: 5591532
PMID: 28886694
DOI: 10.1186/s12864-017-4077-8

[…] as the reads mapped to reference genes or exons. the fpkm (fragments per kb per million of the mapped reads) parameter was employed to count the transcript data [77], whilst the algorithm gfold (generalized fold change) was adopted to produce biological meaning and the rankings of degs [78]. as the recurrent parent of mbi9915 and mbi9749, ccri36 was used to compare the two cssls to generate […]

2017
PMCID: 5591532
PMID: 28886694
DOI: 10.1186/s12864-017-4077-8

[…] (generalized fold change) was adopted to produce biological meaning and the rankings of degs [78]. as the recurrent parent of mbi9915 and mbi9749, ccri36 was used to compare the two cssls to generate gfold value. the genes that their absolute gfold value >1 was defined as degs. furthermore, gene ontology (go) enrichment analysis of degs was performed by blast2go software with corrected p-value  […]

2017
PMCID: 5591532
PMID: 28886694
DOI: 10.1186/s12864-017-4077-8

[…] biological meaning and the rankings of degs [78]. as the recurrent parent of mbi9915 and mbi9749, ccri36 was used to compare the two cssls to generate gfold value. the genes that their absolute gfold value >1 was defined as degs. furthermore, gene ontology (go) enrichment analysis of degs was performed by blast2go software with corrected p-value ≤ 0.5 as the cutoff. kegg pathways of degs […]

GFOLD institution(s)
Department of Bioinformatics, School of Life sciences and Technology, Tongji University, Shanghai, China

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