CisGenome statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Data analysis Peak calling Target gene detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

CisGenome specifications

Information


Unique identifier OMICS_00423
Name CisGenome
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Versioning


Add your version

Maintainers


  • person_outline Wing Hung Wong <>
  • person_outline Hongkai Ji <>
  • person_outline Wenxiu Ma <>

Additional information


http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/manual.htm

Publication for CisGenome

CisGenome in pipelines

 (13)
2017
PMCID: 5321433
PMID: 28225770
DOI: 10.1371/journal.pone.0171508

[…] ab47383), goat anti-foxa2 (santa-cruz; sc-6554), goat anti-hnf1b (santa-cruz; sc-7411) and rabbit anti-hnf1a []., for genechip chip experiments enrichment relative to input dna was determined using cisgenome []. we applied a hidden markov model as described []., cpg island analysis was done using cpgplot in emboss []. we scanned the neurog3 region with a 400 bp sliding window in steps of one […]

2017
PMCID: 5814809
PMID: 29186616
DOI: 10.1093/nar/gkx1190

[…] using macs software (model based analysis of chip-seq) (version 1.4.2) () with a p-value threshold of 1e-5. assigning a binding site to the nearest gene within 100 kb from a peak was performed using cisgenome ver2 (). de novo motif prediction was performed by meme-chip with a slight modification of the default settings (maximum width: 10) (meme-chip version 4.10; […]

2016
PMCID: 4931692
PMID: 27373565
DOI: 10.1038/srep29311

[…] enhancement tool (saet) was used to analyze raw sequence data, including enhancement of color call accuracy and mapping reads to grch37/hg19 by employing lifescope™ genomic analysis software. cisgenome software v2.0 was used to identify binding peaks from mapped reads set at least 30 reads each window and minimum of 30 percent of total reads was limited for each single direction. peaks […]

2016
PMCID: 4949226
PMID: 27486469
DOI: 10.3389/fpls.2016.01055

[…] then, lmfit was used to fit a linear model to the data so statistical calculations could be made using ebayes. chip-chip/seq data was mapped to the tair10 genome using bowtie, analyzed by cisgenome v2.0, and visualized by igv v2.3. gene set enrichment analysis was conducted with the gsea package v2.08 (broad institute, mit) according to the online user guide. acc-responsive gene sets […]

2015
PMCID: 4447067
PMID: 26020590
DOI: 10.1038/srep10469

[…] s were processed using samtools and bedtools. the quality of each sequenced sample was checked using cross-correlation analysis implemented in spp r package. chip-seq peak calling was performed using cisgenome by imposing default parameters. input data (control dna) was used to model the background noise., for all gene expression experiments, bacterial strains were grown in lb medium to od600nm =  […]


To access a full list of citations, you will need to upgrade to our premium service.

CisGenome in publications

 (145)
PMCID: 5919413
PMID: 29698469
DOI: 10.1371/journal.pone.0196400

[…] life technologies, carlsbad, ca, usa). sequencing reads were mapped against the reference genome (hg19,ncbi3) using the bwa package (-c–l 25 –k 2 –n 10) []. non-uniquely placed reads were discarded. cisgenome v2.0 software package [] was used for the peak calling from the chip-seq data with settings–e 50 –maxgap and further analysis. cisgenome 2 was used with settings: -e 50, -maxgap 200 […]

PMCID: 5870497
PMID: 29580210
DOI: 10.1186/s12864-018-4594-0

[…] of putative transcription factor binding sites (tfbs) were found by mapping tfbs motifs identified in drosophila melanogaster to the amel 4.5 version of the honey bee genome using the program cisgenome []. suggestive cpgs identified at minute-120 and tfbs were quantified within each promoter (2 kb upstream of tss) for genes of ogs 3.2. hypergeometric tests were performed to calculate […]

PMCID: 5815144
PMID: 29309682
DOI: 10.1093/nar/gkx1284

[…] non-specific and excluded from subsequent analyses. in addition, peaks corresponding to repeated regions, which could give false positives, were not contemplated either (). on the other hand, cisgenome, an integrated software for processing raw microarray that defines peaks thanks to computing false discovery rates (fdr), was used. recommended normalization parameters for affymetrix […]

PMCID: 5919752
PMID: 29208650
DOI: 10.1534/g3.117.300138

[…] genome using bowtie v2.2.3 () with preset “–sensitive,” resulting in alignment rates of 96.1–99.3%. reanalysis of the data is described below. chip-enriched regions (peaks) were identified using cisgenome v2.0 () and macs2 v2.1.0 (), and their outputs were integrated for downstream analyses (see details in the supplemental material). prediction of dna motifs at potential yrr1-binding sites […]

PMCID: 5814809
PMID: 29186616
DOI: 10.1093/nar/gkx1190

[…] using macs software (model based analysis of chip-seq) (version 1.4.2) () with a p-value threshold of 1e-5. assigning a binding site to the nearest gene within 100 kb from a peak was performed using cisgenome ver2 (). de novo motif prediction was performed by meme-chip with a slight modification of the default settings (maximum width: 10) (meme-chip version 4.10; […]


To access a full list of publications, you will need to upgrade to our premium service.

CisGenome institution(s)
Department of Biostatistics Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Institute for Computational and Mathematical Engineering Stanford University Durand Building, Stanford, CA, USA; Department of Computer Science Stanford University 353 Serra Mall Stanford, CA, USA; Department of Genetics Stanford University School of Medicine, Stanford, CA, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Department of Statistics Stanford University Sequoia Hall, Stanford, CA,USA; Department of Health Research and Policy Stanford University Sequoia Hall, Stanford, CA, USA
CisGenome funding source(s)
Supported by NIH grant HG003903 (WHW), and by NHGRI's ENCODE project (RMM), and partially by the JHSPH Richard L. Gelb Cancer Research Fund.

CisGenome reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CisGenome