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alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis
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>.
Getting started
Package overview
README.md
Amino acid property analysis
Diversity analysis
Fastq
File input and output
Gene usage analysis
Lineage reconstruction
Topology analysis
Alakazam: Amino acid physicochemical property analysis
Alakazam: Analysis of clonal abundance and diversity
Alakazam: Gene usage analysis
Alakazam: How to read and write files
Alakazam: Reconstruction of Ig lineage trees
Alakazam: Topology analysis of lineage trees
Alakazam: Using sequencing quality scores
Browse package contents
Package details |
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| Author | Susanna Marquez [cre, aut], Namita Gupta [aut], Nima Nouri [aut], Ruoyi Jiang [aut], Julian Zhou [aut], Kenneth Hoehn [aut], Daniel Gadala-Maria [ctb], Edel Aron [ctb], Cole Jensen [ctb], Jason Vander Heiden [aut], Steven Kleinstein [aut, cph] |
| Bioconductor views | AnnotationData Software |
| Maintainer | Susanna Marquez <susanna.marquez@yale.edu> |
| License | AGPL-3 |
| Version | 1.3.0 |
| URL | https://alakazam.readthedocs.io/ |
| Package repository | View on CRAN |
| Installation |
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