alakazam-package

Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) tools:::Rd_expr_doi("10.1093/bioinformatics/btv359"), Stern, Yaari and Vander Heiden, et al (2014) tools:::Rd_expr_doi("10.1126/scitranslmed.3008879").

internal

Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.

Susanna Marquez

alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

Namita Gupta

Nima Nouri

Ruoyi Jiang

Julian Zhou

Kenneth Hoehn

Daniel Gadala-Maria

Edel Aron

Cole Jensen

Gisela Gabernet

Caroline Sullivan

Hailong Meng

Huimin Lyu

Burhan Sabuwala

Jason Vander Heiden

Steven Kleinstein

alakazam-package function

Maintainer: Susanna Marquez <a href="/link/susanna.marquez%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::susanna.marquez@yale.edu">susanna.marquez@yale.edu</a>
Authors:<ul>
<li>Susanna Marquez <a href="/link/susanna.marquez%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::susanna.marquez@yale.edu">susanna.marquez@yale.edu</a></li>
<li>Namita Gupta <a href="/link/namita.gupta%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::namita.gupta@yale.edu">namita.gupta@yale.edu</a></li>
<li>Nima Nouri <a href="/link/nima.nouri%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::nima.nouri@yale.edu">nima.nouri@yale.edu</a></li>
<li>Ruoyi Jiang <a href="/link/ruoyi.jiang%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::ruoyi.jiang@yale.edu">ruoyi.jiang@yale.edu</a></li>
<li>Julian Zhou <a href="/link/julian.zhou%40bulldogs.yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::julian.zhou@bulldogs.yale.edu">julian.zhou@bulldogs.yale.edu</a></li>
<li>Kenneth Hoehn <a href="/link/kenneth.hoehn%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::kenneth.hoehn@yale.edu">kenneth.hoehn@yale.edu</a></li>
<li>Cole Jensen <a href="/link/cole.jensen%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::cole.jensen@yale.edu">cole.jensen@yale.edu</a></li>
<li>Jason Vander Heiden <a href="/link/jason.vanderheiden%40gmail.com?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::jason.vanderheiden@gmail.com">jason.vanderheiden@gmail.com</a></li>
<li>Steven Kleinstein <a href="/link/steven.kleinstein%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::steven.kleinstein@yale.edu">steven.kleinstein@yale.edu</a> [copyright holder]</li>
</ul>Other contributors:<ul>
<li>Daniel Gadala-Maria <a href="/link/daniel.gadala-maria%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::daniel.gadala-maria@yale.edu">daniel.gadala-maria@yale.edu</a> [contributor]</li>
<li>Edel Aron <a href="/link/edel.aron%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::edel.aron@yale.edu">edel.aron@yale.edu</a> [contributor]</li>
<li>Gisela Gabernet <a href="/link/gisela.gabernet%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::gisela.gabernet@yale.edu">gisela.gabernet@yale.edu</a> [contributor]</li>
<li>Caroline Sullivan <a href="/link/caroline.sullivan%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::caroline.sullivan@yale.edu">caroline.sullivan@yale.edu</a> [contributor]</li>
<li>Hailong Meng <a href="/link/hailong.meng%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::hailong.meng@yale.edu">hailong.meng@yale.edu</a> [contributor]</li>
<li>Huimin Lyu <a href="/link/huimin.lyu%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::huimin.lyu@yale.edu">huimin.lyu@yale.edu</a> [contributor]</li>
<li>Burhan Sabuwala <a href="/link/burhan.sabuwala%40yale.edu?package=alakazam&version=1.5.0" data-mini-rdoc="alakazam::burhan.sabuwala@yale.edu">burhan.sabuwala@yale.edu</a> [contributor]</li>
</ul>

Author

alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis — alakazam-package

Maintainer: Susanna Marquez <a href='mailto:susanna.marquez@yale.edu'>susanna.marquez@yale.edu</a>
Authors:<ul>
<li>Susanna Marquez <a href='mailto:susanna.marquez@yale.edu'>susanna.marquez@yale.edu</a></li>
<li>Namita Gupta <a href='mailto:namita.gupta@yale.edu'>namita.gupta@yale.edu</a></li>
<li>Nima Nouri <a href='mailto:nima.nouri@yale.edu'>nima.nouri@yale.edu</a></li>
<li>Ruoyi Jiang <a href='mailto:ruoyi.jiang@yale.edu'>ruoyi.jiang@yale.edu</a></li>
<li>Julian Zhou <a href='mailto:julian.zhou@bulldogs.yale.edu'>julian.zhou@bulldogs.yale.edu</a></li>
<li>Kenneth Hoehn <a href='mailto:kenneth.hoehn@yale.edu'>kenneth.hoehn@yale.edu</a></li>
<li>Cole Jensen <a href='mailto:cole.jensen@yale.edu'>cole.jensen@yale.edu</a></li>
<li>Jason Vander Heiden <a href='mailto:jason.vanderheiden@gmail.com'>jason.vanderheiden@gmail.com</a></li>
<li>Steven Kleinstein <a href='mailto:steven.kleinstein@yale.edu'>steven.kleinstein@yale.edu</a> [copyright holder]</li>
</ul>

Other contributors:<ul>
<li>Daniel Gadala-Maria <a href='mailto:daniel.gadala-maria@yale.edu'>daniel.gadala-maria@yale.edu</a> [contributor]</li>
<li>Edel Aron <a href='mailto:edel.aron@yale.edu'>edel.aron@yale.edu</a> [contributor]</li>
<li>Gisela Gabernet <a href='mailto:gisela.gabernet@yale.edu'>gisela.gabernet@yale.edu</a> [contributor]</li>
<li>Caroline Sullivan <a href='mailto:caroline.sullivan@yale.edu'>caroline.sullivan@yale.edu</a> [contributor]</li>
<li>Hailong Meng <a href='mailto:hailong.meng@yale.edu'>hailong.meng@yale.edu</a> [contributor]</li>
<li>Huimin Lyu <a href='mailto:huimin.lyu@yale.edu'>huimin.lyu@yale.edu</a> [contributor]</li>
<li>Burhan Sabuwala <a href='mailto:burhan.sabuwala@yale.edu'>burhan.sabuwala@yale.edu</a> [contributor]</li>
</ul>

alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

alakazam-package: alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Description

Arguments

Author

See Also