Protocols

BIDCHIPS specifications

Information


Unique identifier OMICS_10666
Name BIDCHIPS
Alternative name BIas Decomposition of CHIP-seq Signals
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, R
Computer skills Advanced
Stability No
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Parameswaran Ramachandran
  • person_outline Theodore Perkins

Publication for BIas Decomposition of CHIP-seq Signals

BIDCHIPS citation

call_split

Reprogramming progeria fibroblasts re‐establishes a normal epigenetic landscape

2017
Aging Cell
PMCID: 5506428
PMID: 28597562
DOI: 10.1111/acel.12621
call_split See protocol

[…] fReps (Shen et al., ) was used to identify genomic regions differentially enriched for H3K27me3 and H3K4me3. ChIP‐seq BAM files reads were converted to BED files. Fragment lengths used for input into BIDCHIPS were the average of the fragment lengths of the treatment and control files as estimated by MaSC (Ramachandran et al., ). The different histones were analyzed with parameters as recommended i […]

BIDCHIPS institution(s)
Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
BIDCHIPS funding source(s)
Supported in part by grants from the Natural Sciences and Engineering Research Council of Canada (NSERC), the Government of Ontario Ministry of Economic Development and Innovation (MEDI), the Ottawa Hospital Research Institute (OHRI), and the US National Institutes of Health (NIH).

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