Glbase protocols

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Glbase specifications

Information


Unique identifier OMICS_17650
Name Glbase
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
Numpy, Scipy, Matplotlib
Maintained Yes

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Publication for Glbase

Glbase in pipeline

2017
PMCID: 5610324
PMID: 28939884
DOI: 10.1038/s41467-017-00668-4

[…] for grch38/hg38 using rsem (rsem-1.2.4), bowtie2 (v2.2.5), and normalized with edaseq (v2.2.0). gene expression is expressed as “normalized tag count.” other downstream analyses were performed using glbase. in brief, differential expression between differentiation state and the esc control was analyzed using the edger package, where raw read counts per gene were normalized using trimmed mean […]


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Glbase in publications

 (11)
PMCID: 5865784
PMID: 28901433
DOI: 10.3892/mmr.2017.7465

[…] gene product attributes. the-log10 (p-value) demonstrated the significance of go term enrichment in the differentially expressed mrna list. all other bioinformatic analysis was performed using glbase ()., all assays were expressed as the mean ± standard deviation from at least three separate experiments using spss 13.0 (spss inc., chicago, il, usa). gene expression levels in osteogenic […]

PMCID: 5418622
PMID: 28466868
DOI: 10.1038/ncomms15166

[…] of 2 million sequence tags. reads were aligned to the ensembl (mm10 v76) transcriptome using bowtie2 (v2.2.0) and rsem (v1.2.17), gc-normalized using edaseq (v2.0.0). analysis was performed using glbase. reads were deposited with geo under the accession number gse70741., single-cell qpcr was performed using a fluidigm c1 and biomark hd as described by the manufacturer. briefly, a cell […]

PMCID: 5389706
PMID: 28426095
DOI: 10.1093/nar/gkx054

[…] based on weak (r2 > 0.55) or strong (r2 > 0.8) correlations. all networks were laid out using ‘neato’ (http://graphviz.org/) and the analysis was performed using the ‘network’ module of glbase (). pca was performed using the ‘pca’ module of glbase (), which relies on sklearn pca function. soms and pca were constructed using a filtered set of genes (), the mds to seed the som […]

PMCID: 5106517
PMID: 27746115
DOI: 10.1016/j.stemcr.2016.09.008

[…] if they had a benjamini-hochberg corrected p value (q value) <0.1 and had a fold-change > 1.5. gene ontology was performed using goseq (v1.20.0). other analyses were performed using glbase ()., endothelial cell-related assays, including endothelial cell culture, dii-ac-ldl uptake, and capillary structure formation, were performed as described previously (). in brief, the egfp+ […]

PMCID: 4868314
PMID: 27183310
DOI: 10.1371/journal.pone.0154939

[…] through the illuminehiseq2500. data was aligned to the ensembl transcript annotations using bowtie and rsem as described previously []. all other bioinformatics analysis was performed using glbase []., results were analyzed with spss 21.0 statistical software. student’s t test was used to evaluate the quantitative variables. pearson test or correction for continuity chi square test […]


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Glbase institution(s)
Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Genome Regulation Laboratory, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, China; Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Institute of Cellular Medicine, Newcastle University Medical School, Newcastle upon Tyne, UK

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