CisGenome Browser protocols

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CisGenome Browser specifications

Information


Unique identifier OMICS_22151
Name CisGenome Browser
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A sample file.
Input format BAR,TSV,BAM,refFlat,UCSC BED,WIG
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Version 1.0.14
Stability Stable
Source code URL http://www-personal.umich.edu/~jianghui/browser/download/cisgenomebrowser-1.1.3-src.zip
Maintained Yes

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Maintainers


  • person_outline Hui Jiang <>
  • person_outline Hui Jang <>

Additional information


http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/tutorial_visualization.htm http://www-personal.umich.edu/~jianghui/browser/README.html#acknowledgements

Publication for CisGenome Browser

CisGenome Browser in pipeline

2014
PMCID: 4190017
PMID: 25173176
DOI: 10.1038/nsmb.2881

[…] on an agilent bioanalyzer. sequencing was performed on an illumina gxii or hiseq 2000 or solid. raw reads were mapped to the reference genome (saccer2) by bowtie and peaks were visualized by the cisgenome browser as described above., information on tss locations was adopted from a previous study. tsss of genes of interest were aligned at zero of x-axis and chip-seq reads were counted […]


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CisGenome Browser in publications

 (5)
PMCID: 5634782
PMID: 28949295
DOI: 10.7554/eLife.29938.025

[…] and quantified on an agilent bioanalyzer. sequencing was performed on illumina hiseq platform. raw reads were mapped to the reference genome (saccer2) by bowtie () and peaks were visualized by the cisgenome browser ()., acetyl-coa was extracted with two methods. for the first method, na azide was added (10 mm) and 5 od cells were spun down and lysed in 200 µl of 10% perchloric acid by bead […]

PMCID: 5093089
PMID: 27132513
DOI: 10.1038/onc.2016.112

[…] a few hundred dna base pairs. in our study, the default setting was selected, which is commonly utilized and suitable to our datasets. detected peak regions were visualized mainly by using the cisgenome browser () together with gene structure, dna sequences and conservation scores. we compared the fraction of peaks residing in various genomic features with the corresponding genome […]

PMCID: 4190017
PMID: 25173176
DOI: 10.1038/nsmb.2881

[…] genes were defined from the sgd annotation file of 20100102 corresponding to the mapping index. (http://downloads.yeastgenome.org/curation/chromosomal_feature/ ). to display rna signals in the cisgenome browser, rnaseq data was first mapped to saccer2 by bowtie (-5 3 -3 8 –best saccer2). results were imported into cisgenome browser package and were displayed in 20 bp windows […]

PMCID: 3892789
PMID: 24222491
DOI: 10.1128/mBio.00869-13

[…] hits per kb of coding dna were considered in analyses. signal intensities were visualized graphically by converting maq-aligned reads into a bar file using cisgenome software and viewed on the cisgenome browser (stanford university, stanford, ca) (). for a smoother graphical display of data, a moving average of reads per 200-bp sliding nucleotide window was generated using the matlab […]

PMCID: 3510170
PMID: 23209612
DOI: 10.1371/journal.pone.0049887

[…] . tc-ar binding regions were identified by comparison to total input control as well as igg control using the tilemap peak detection tool . genomic locations of binding peaks were visualized in the cisgenome browser., ln/tc-ar is a newly developed cell line derived from the parental lncap line in which a truncated form of the androgen receptor (tc-ar) is expressed following doxycycline […]


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CisGenome Browser institution(s)
Department of Statistics, Stanford University, Stanford, CA, USA; Stanford Genome Technology Center, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Systems Biology Centre, Coventry House, the University of Warwick, Coventry, UK; Department of Health Research and Policy, Stanford University, Stanford, CA, USA
CisGenome Browser funding source(s)
Supported by National Institute of Health grant R01-HG004634; in part by National Institute of Health grant 2P01-HG000205; and Agilent Technologies.

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