Array Suite statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Array Suite
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Tool usage distribution map

This map represents all the scientific publications referring to Array Suite per scientific context
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Associated diseases

This word cloud represents Array Suite usage per disease context
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Popular tool citations

chevron_left Read quality control Normalization Known transcript quantification Bioinformatics workflows Gene fusion detection Differential expression Bioinformatics workflows Bioinformatics workflows Bioinformatics workflows Alternative splicing events identification Spliced read alignment Variant detection Gene expression visualization chevron_right
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Protocols

Array Suite specifications

Information


Unique identifier OMICS_00850
Name Array Suite
Alternative names ArrayStudio, Array Studio, ArrayServer, Array Server, GenomeBrowser, Genome Browser, Oshell, ArrayLand, Array Land
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences
Operating system Unix/Linux
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Array Studio

Additional information


http://www.arrayserver.com/wiki/index.php?title=Array_Suite_Wiki

Publication for Array Suite

Array Suite citations

 (57)
library_books

Transcriptome Analysis of Orbital Adipose Tissue in Active Thyroid Eye Disease Using Next Generation RNA Sequencing Technology

2018
PMCID: 5906971
PMID: 29760827
DOI: 10.2174/1874364101812010041

[…] ease-free water. Output data was analyzed by a professional senior bioinformatics engineer at the UCSD Center for Computational Biology and Bioinformatics. Ribosomal RNA filtering was performed using Array Studio NGS analytics (http://www.omicsoft.com/array-studio) and demonstrated successful ribosomal RNA depletion with only 1.5 to 3.8% rRNA sequences filtered. The Array Studio Raw Data QC Wizard […]

call_split

Glucagon contributes to liver zonation

2018
Proc Natl Acad Sci U S A
PMCID: 5924920
PMID: 29555772
DOI: 10.1073/pnas.1721403115
call_split See protocol

[…] were decoded based on their barcodes and read quality was evaluated with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the mouse transcriptome (NCBI GRCm38) using ArrayStudio software (OmicSoft) allowing two mismatches. Reads mapped to the exons of a gene were summed at the gene level. Differentially expressed genes were identified by the DESeq2 package and sig […]

call_split

RPE phagocytic function declines in age related macular degeneration and is rescued by human umbilical tissue derived cells

2018
J Transl Med
PMCID: 5851074
PMID: 29534722
DOI: 10.1186/s12967-018-1434-6
call_split See protocol

[…] aries were prepared using Illumina’s TruSeq total RNA Sample Prep kit following the manufacturer’s instructions, and sequenced with Illumina’s HiSeq 2000. All RNA sequencing data were processed using ArrayStudio tool (Omicsoft, Cary, NC). Human sequence reads were mapped onto genome assembly GRCh38 (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/).refGene gene model (http://genome. […]

call_split

Bronchial extracellular matrix from COPD patients induces altered gene expression in repopulated primary human bronchial epithelial cells

2018
Sci Rep
PMCID: 5823945
PMID: 29472603
DOI: 10.1038/s41598-018-21727-w
call_split See protocol

[…] 0.6 M mapped reads (10.8 M on average) with a 97% mapping frequency or higher per sample. Gene level quantifications and counts were generated with featurecounts (version 1.4.4) within bcbio-nextgen. ArrayStudio version 9 (OmicSoft, Cary, NC) was used for further data analysis. Heatmaps were created based on hierarchical clustering of log2-transformed ratios (COPD/normal) of DESeq2-normalized coun […]

library_books

Meta analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets

2018
BMC Syst Biol
PMCID: 5763539
PMID: 29321020
DOI: 10.1186/s12918-017-0524-z

[…] 3) each patient and control group had at least three samples.Raw gene expression data, study design table and annotation table of each dataset were obtained from the GEO database and processed using ArrayStudio v8.0 (OmicSoft, USA). All datasets retrieved are microarray datasets except for GSE41055, which is an exon array and was excluded from further analysis. Several datasets (GSE42834, GSE5615 […]

library_books

Integrative network analysis highlights biological processes underlying GLP 1 stimulated insulin secretion: A DIRECT study

2018
PLoS One
PMCID: 5749727
PMID: 29293525
DOI: 10.1371/journal.pone.0189886

[…] nst the mouse reference genome b38.1 with RefSeq as the gene model as implemented in OmicSoft® ArraySuite® software, version 8. RNA transcripts were quantified using RSEM methods [] as implemented in Arraystudio counting count the read fragments mapping to each individual gene and quantify expression by the corresponding FPKM. In summary, expression was measured as FPKM for 25,054 unique genes. Pr […]


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Array Suite institution(s)
Division of Bioinformatics, Omicsoft Inc., Cary, NC, USA; Bioinformatics Research Center, North Carolina State University, Ricks Hall, Raleigh, NC, USA; Genome Analysis Unit, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, USA

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