CHANCE specifications

Information


Unique identifier OMICS_00429
Name CHANCE
Alternative name CHIP-seq ANalytics and Confidence Estimation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Jun Song
  • person_outline Aaron Diaz

Publication for CHIP-seq ANalytics and Confidence Estimation

CHANCE citations

 (2)
library_books

Identification of cis regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response

2017
PLoS One
PMCID: 5640250
PMID: 29028826
DOI: 10.1371/journal.pone.0186435

[…] 7 301 q30 unique reads. Unique non-duplicated aligned sequence tags were used for open chromatin site peak calling. Prior to peak calling, aligned and filtered sequence tag datasets were validated by CHip-seq ANalytics and Confidence Estimation (CHANCE) software (https://github.com/songlab/chance). […]

library_books

Epigenomic profiling of primary gastric adenocarcinoma reveals super enhancer heterogeneity

2016
Nat Commun
PMCID: 5052795
PMID: 27677335
DOI: 10.1038/ncomms12983

[…] icating successful enrichment. A similar analysis was also performed for the H3K4me3 libraries (a promoter mark), and all 42 libraries satisfied this quality control criteria. Second, we used CHANCE (CHip-seq ANalytics and Confidence Estimation), a software for ChIP-seq quality control and protocol optimization that indicates whether a library shows successful or weak enrichment. We found that the […]

CHANCE institution(s)
Institute for Human Genetics, UCSF, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
CHANCE funding source(s)
Supported by grants from the Sontag Foundation and the National Cancer Institute (R01CA163336).

CHANCE review

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Fabien Pichon

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Desktop
Not ideal to me because as far as I know, it's impossible to use it with command line... I had difficulties to open .bam files...