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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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Documentation


Publication for Generalized fold change

GFOLD citations

 (43)
library_books

The thioredoxin 1 system is essential for fueling DNA synthesis during T cell metabolic reprogramming and proliferation

2018
Nat Commun
PMCID: 5945637
PMID: 29749372
DOI: 10.1038/s41467-018-04274-w

[…] n SEB administration but not in the PBS-treated group, indicating defective expansion in the absence of Txnrd1 (Fig.  and Supplementary Fig. ).Fig. 6Among the top differentially expressed gene sets (|GFOLD| > 1.5; false discovery rate [FDR] < 0.2) between SEB-stimulated Txnrd1-deficient and control T cell groups, the cell cycle inhibitor Cdkn1a (the gene encoding p21; FDR = 0.05) was significantly […]

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Transcriptional regulation of P63 on the apoptosis of male germ cells and three stages of spermatogenesis in mice

2018
PMCID: 5833356
PMID: 29362488
DOI: 10.1038/s41419-017-0046-z
call_split See protocol

[…] data. Clean reads were obtained after the raw reads were filtered with adaptor skewer, and sequencing data were mapped to mouse genome mm10 RefSeq with Tophat version 2.0.13 with default parameters. Gfold version 1.1.2 was used to produce biologically meaningful rankings of differentially expressed genes (DEGs). Subsequently, those DEGs were assessed by Audics using RPKM, and the significantly DE […]

library_books

Isoform Sequencing and State of Art Applications for Unravelling Complexity of Plant Transcriptomes

2018
Genes
PMCID: 5793194
PMID: 29346292
DOI: 10.3390/genes9010043

[…] er the biological functions of AS and APA events [], whereas Iso-Seq data could also be used to measure the gene expression level with counting full-length transcripts at whole transcriptional level. GFOLD, which is specifically designed for data without biological replicates is used to search for differentially expressed genes between different samples []. Using GFOLD, 186 differentially expresse […]

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The prolyl isomerase FKBP25 regulates microtubule polymerization impacting cell cycle progression and genomic stability

2018
Nucleic Acids Res
PMCID: 5861405
PMID: 29361176
DOI: 10.1093/nar/gky008
call_split See protocol

[…] ing system (Illumina). Paired-end reads were aligned to the UCSC hg19 human reference genome using the HISAT2 alignment program (). Ranked lists of differentially expressed genes were generated using GFOLD (). 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 version 6.8) w […]

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ERK inhibition represses gefitinib resistance in non small cell lung cancer cells

2018
Oncotarget
PMCID: 5844726
PMID: 29552290
DOI: 10.18632/oncotarget.24147
call_split See protocol

[…] The RNA-Seq reads were aligned to the hg19 genome assembly using TopHat (version 1.1.4) with the default parameters []. The expression index was generated using GFOLD V1.1.3 job count [] from the bam files from TopHat. The differentially expressed genes were ranked using GFOLD V1.1.3 job diff []. The final output file contains all genes with a GFOLD value, wh […]

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Transcriptome response of Atlantic salmon (Salmo salar) to competition with ecologically similar non‐native species

2018
Ecol Evol
PMCID: 5792521
PMID: 29435251
DOI: 10.1002/ece3.3798
call_split See protocol

[…] Huber, & Anders, ). For the supervised approach, we tested for transcriptomic response to competition with the three different non‐native salmonid species within each Atlantic salmon population using GFOLD V1.1.3 (Feng et al., ). GFOLD can analyze RNA‐Seq data with biological replicates or one treatment without replicates within a reliable statistical framework (Feng et al., ). To prepare gene exp […]

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

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