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Number of citations per year for the bioinformatics software tool Change-O
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chevron_left Selection pressure quantification Mutation profiling V(D)J gene usage Germline reconstruction Clonal lineage reconstruction Clonal clustering CDR3 sequence identification chevron_right
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Protocols

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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Maintainer


  • person_outline Steven Kleinstein

Publication for Change-O

Change-O citations

 (66)
library_books

Computational Strategies for Dissecting the High Dimensional Complexity of Adaptive Immune Repertoires

2018
Front Immunol
PMCID: 5826328
PMID: 29515569
DOI: 10.3389/fimmu.2018.00224

[…] l be 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 o […]

library_books

High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis

2018
BMC Genomics
PMCID: 5811979
PMID: 29439658
DOI: 10.1186/s12864-018-4512-5

[…] onstant 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 []. […]

library_books

Association of Air Pollution Exposure and Interleukin 13 Haplotype with the Risk of Aggregate Bronchitic Symptoms in Children

2018
PMCID: 5925581
PMID: 29456163
DOI: 10.1016/j.ebiom.2018.02.008

[…] pollutants concentrations were presented in . There were significantly positive associations between chronic phlegm without asthma and exposure to PM2.5 (aOR, 1.59; 95% CI, 1.07–2.37 per 12.51 μg/m3 change), O3 (aOR, 1.54 95% CI, 1.05–2.27 per 8.28 ppb change) and SO2 (aOR, 1.19; 95% CI, 1.02–1.39 per 0.98 ppb change). Although the OR of exposure to PM2.5, O3 and SO2 was elevated, we did not iden […]

call_split

Functionally Convergent B Cell Receptor Sequences in Transgenic Rats Expressing a Human B Cell Repertoire in Response to Tetanus Toxoid and Measles Antigens

2017
Front Immunol
PMCID: 5743747
PMID: 29312330
DOI: 10.3389/fimmu.2017.01834
call_split See protocol

[…] ber: 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. […]

library_books

Cooperative polariton dynamics in feedback coupled cavities

2017
Nat Commun
PMCID: 5681655
PMID: 29127391
DOI: 10.1038/s41467-017-01796-7

[…] behavior of coupled harmonic oscillators, . In the linear dynamic regime where the number of CMP m≪N, the spin ensemble is far from being saturated, so that adding photons may increase m but does not change Ω 0. Hence, in contrast to quantum systems, the magnon-photon cooperativity, C≡2(Ω0∕ωc)2Q∕α, has been found to be independent of photon number. Breaking such a harmonic limit without interferin […]

library_books

The Potential Liver, Brain, and Embryo Toxicity of Titanium Dioxide Nanoparticles on Mice

2017
PMCID: 5540742
PMID: 28774157
DOI: 10.1186/s11671-017-2242-2

[…] We 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. Nor did it change […]


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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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