alakazam statistics

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alakazam specifications


Unique identifier OMICS_21399
Name alakazam
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Other
Computer skills Advanced
Stability No
Maintained No



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alakazam in publications

PMCID: 5110968
PMID: 27849037
DOI: 10.1038/srep37229

[…] pcr error, only clusters containing at least 50 sequences were used to create lineage trees. subsampling down to 50 sequences was performed if there were more. lineage trees were created using the alakazam software package., statistics were performed using r; specific tests used are detailed in the figure legends. repertoire diversity, and lineage diversity were calculated using the shannon […]

PMCID: 5021391
PMID: 27466419
DOI: 10.1128/JVI.01089-16

[…] for mouse 2 for detailed investigation. downstream analyses were performed using tools from the change-o suite (version 0.3.3-2016.04.22) and the associated r packages shazam (shazam_0.1.2.999) and alakazam (alakazam_0.2.3.999) (). detailed information is available at sequences were assigned to the same clone when they shared the same ighv gene, ighj gene, […]

PMCID: 4973324
PMID: 27525066
DOI: 10.1038/cti.2016.42

[…] furthermore, clustering was used to counteract potential dominance of expanded b-cell clones, and to eliminate sequence errors that arose during amplification and sequencing. we used the r-package alakazam in order to characterize clustered populations by calculating the hill diversity indices, as well as shannon's entropy and evenness metrics ()., all statistical analyses were performed […]

PMCID: 4910312
PMID: 27312086
DOI: 10.1186/s13073-016-0322-z

[…] the prcomp function in the “stats” package []. rarefaction analysis was conducted using the “inext” package [] using a q value of 0., lineage trees were constructed from sequence clusters using the “alakazam” package []. lineages were only generated for clusters with at least 50 or 25 sequences depending on the analysis, and subsampling was performed if there were more than this number. […]

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alakazam institution(s)
Yale University
alakazam funding source(s)
This work was supported by the National Institutes of Health [R01AI104739 to S.H.K.; T15LM07056 to N.T.G., T15LM07056 to J.A.V.H. from National Library of Medicine (NLM)] and by the United States-Israel Binational Science Foundation [2013395 to G.Y. and S.H.K.].

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