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Citations per year

Number of citations per year for the bioinformatics software tool Glbase
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This map represents all the scientific publications referring to Glbase per scientific context
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Protocols

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 citations

 (8)
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PRC2 specifies ectoderm lineages and maintains pluripotency in primed but not naïve ESCs

2017
Nat Commun
PMCID: 5610324
PMID: 28939884
DOI: 10.1038/s41467-017-00668-4
call_split See protocol

[…] 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 of M […]

call_split

A sequential EMT MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes

2017
Nat Commun
PMCID: 5418622
PMID: 28466868
DOI: 10.1038/ncomms15166
call_split See protocol

[…] pth 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. […]

call_split

Models of global gene expression define major domains of cell type and tissue identity

2017
Nucleic Acids Res
PMCID: 5389706
PMID: 28426095
DOI: 10.1093/nar/gkx054
call_split See protocol

[…] nodes (C/Ts), 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 training […]

call_split

Generation and Analysis of GATA2w/eGFP Human ESCs Reveal ITGB3/CD61 as a Reliable Marker for Defining Hemogenic Endothelial Cells during Hematopoiesis

2016
Stem Cell Reports
PMCID: 5106517
PMID: 27746115
DOI: 10.1016/j.stemcr.2016.09.008
call_split See protocol

[…] dered significant 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 (). […]

call_split

Increased Expression of SETD7 Promotes Cell Proliferation by Regulating Cell Cycle and Indicates Poor Prognosis in Hepatocellular Carcinoma

2016
PLoS One
PMCID: 4868314
PMID: 27183310
DOI: 10.1371/journal.pone.0154939
call_split See protocol

[…] Guangzhou 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 []. […]

library_books

Optimized Approaches for Generation of Integration free iPSCs from Human Urine Derived Cells with Small Molecules and Autologous Feeder

2016
Stem Cell Reports
PMCID: 4939659
PMID: 27132887
DOI: 10.1016/j.stemcr.2016.04.001

[…] the TruSeq RNA Sample Preparation Kit v2 (Illumina). Libraries were sequenced using MiSeq Reagent Kit v2. Hierarchical clustering of the RNA-seq data, heatmaps, and scatterplots were generated using glbase (). […]


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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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