recipe r-alakazam

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>.

Homepage:

http://alakazam.readthedocs.org

License:

AGPL / AGPL-3

Recipe:

/r-alakazam/meta.yaml

package r-alakazam

Versions:

1.2.1-1,  1.2.1-0,  1.2.0-1,  1.2.0-0,  0.2.10-0,  0.2.8-0,  0.2.7-0

Depends:

• bioconductor-biostrings >=2.56.0

• bioconductor-genomicalignments >=1.24.0

• bioconductor-iranges >=2.22.2

• libgcc-ng >=12

• libstdcxx-ng >=12

• r-airr >=1.3

• r-ape

• r-base >=4.2,<4.3.0a0

• r-dplyr >=1.0

• r-ggplot2 >=3.3.4

• r-igraph >=1.0.0

• r-matrix

• r-progress

• r-rcpp >=0.12.12

• r-readr

• r-rlang

• r-scales

• r-seqinr

• r-stringi

• r-tibble

• r-tidyr >=1.0

Required By:

• r-scoper

• r-shazam

• r-enchantr

• r-prestor

• igphyml

• r-dowser

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install r-alakazam

and update with:

conda update r-alakazam

or use the docker container:

docker pull quay.io/biocontainers/r-alakazam:<tag>

(see r-alakazam/tags for valid values for <tag>)

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