IGB protocols

IGB specifications

Information


Unique identifier OMICS_00916
Name IGB
Alternative name Integrated Genome Browser
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Common Public License Version 1.0
Computer skills Medium
Version 9.0.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Integrated_Genome_Browser

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Maintainer


  • person_outline Ann Loraine <>

Publications for Integrated Genome Browser

IGB IN pipelines

 (11)
2016
PMCID: 4886428
PMID: 27245778
DOI: 10.1186/s13073-016-0315-y

[…] were analyzed using the standard tophat/cufflinks pipeline [42]. for chip-seq and gro-seq (global run-on sequencing) data an integrative analysis pipeline was applied [43]. data were visualized in integrated genome browser [44]., chip was performed as previously described with minor modifications [45]. briefly, cells were crosslinked with dsg (sigma) for 30 minutes and then with formaldehyde […]

2016
PMCID: 5009733
PMID: 27235415
DOI: 10.1093/nar/gkw466

[…] the highest score and a maximum of two mismatches. read mappings were processed using samtools (24), and coverage graphs were extracted using bedtools (25). coverage graphs were visualized using the integrated genome browser (26). the 5′ sharpness of cosrnas that are positioned at 3′-ends of mitochondrial and plastid transcripts was calculated as the number of nucleotides required to decrease […]

2015
PMCID: 4304717
PMID: 25615622
DOI: 10.1371/journal.pgen.1004944

[…] reads were retained for further analysis. then the data were analyzed as described [19]. briefly, the alignments were first converted to wig files using macs [74]. then the data were imported to integrated genome browser (igb) [75] for visualization. secondly, the program sicer [76] was used to identify chip-enriched domains (peaks) in histone modification signals. thirdly, quantitative […]

2015
PMCID: 4304717
PMID: 25615622
DOI: 10.1371/journal.pgen.1004944

[…] further analysis. then the data were analyzed as described [19]. briefly, the alignments were first converted to wig files using macs [74]. then the data were imported to integrated genome browser (igb) [75] for visualization. secondly, the program sicer [76] was used to identify chip-enriched domains (peaks) in histone modification signals. thirdly, quantitative comparisons between wild-type […]

2015
PMCID: 4591623
PMID: 26427366
DOI: 10.1186/s12896-015-0207-z

[…] analysis results and data are available on-line at the project repository web site. alignments from tophat, coverage graphs, and assembled reads (from cufflinks) are available for visualization in integrated genome browser [46] from the igbquickload site [http://igbquickload.org/soy]., for this study we chose seed tissue derived from three independent transgenic lines expressing different […]

IGB institution(s)
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC, USA
IGB funding source(s)
Supported by the National Institutes of Health [R01GM103463].

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