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Change-O specifications

Information


Unique identifier OMICS_08874
Name Change-O
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Steven Kleinstein <>

Publication for Change-O

Change-O in publications

 (17)
PMCID: 5826328
PMID: 29515569
DOI: 10.3389/fimmu.2018.00224

[…] needed to establish reliable guidelines for diversity estimation., to compare differences between diversity profiles, one should also consider resampling strategies as implemented in the r package change-o by gupta et al. these allow the determination of confidence areas around each diversity profile (, ) in the presence of differently sized repertoires. accurate diversity calculation in case […]

PMCID: 5811979
PMID: 29439658
DOI: 10.1186/s12864-018-4512-5

[…] region sequence were then annotated using igblast []. variable (v), diversity (d), joining (j), and complementarity determining region (cdr) calls were extracted from the igblast output using change-o []., additional file 1: additional file 2: additional file 3: additional file 4: additional file 5: additional file 6: additional file 7: additional file 8: additional file 9: , electronic […]

PMCID: 5743747
PMID: 29312330
DOI: 10.3389/fimmu.2017.01834

[…] srp068407 ()]. samples taken at day 7 post immunization were excluded to avoid skewing of data distributions by the applied vaccination. samples were annotated using imgt and postprocessed using change-o framework [v 0.2.4 ()]. only functional sequences present at least three times per data set were considered for assessing cdr3 length distributions and somatic hypermutation level., […]

PMCID: 5540742
PMID: 28774157
DOI: 10.1186/s11671-017-2242-2

[…] determined the effects of nano-tio2 on the redox state and signal molecules in brain tissue of mice exposed to nano-tio2 (i.p. for 14 days). we observed that a low dose (5 mg/kg) nano-tio2 did not change o2−, h2o2 and mda levels, did not change the activities of the antioxidant enzymes apx, cat, gshpx, and sod, or the levels of non-enzymatic antioxidants asa/dasa and gsh/gssg. […]

PMCID: 5519504
PMID: 28709802
DOI: 10.1016/j.immuni.2017.06.013

[…] (table s3). paired-end raw sequencing reads were processed into donor-specific ig gene sequences and grouped in clonal families using a bioinformatics pipeline based on presto, igblast and change-o (, , ). first, raw reads with a phred score lower than 20 were filtered out, and primers for ch and vh genes were masked. next, corresponding paired-end reads were aligned and merged […]


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Change-O institution(s)
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA; Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
Change-O funding source(s)
Supported by the National Institutes of Health [R01AI104739; T15LM07056, T15LM07056 from National Library of Medicine (NLM)] and by the United States-Israel Binational Science Foundation [2013395].

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