recipe r-scoper

Provides a computational framework for identification of B cell clones from Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main functions are included (identicalClones, hierarchicalClones, and spectralClones) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>. Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>. Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.

Homepage:

https://scoper.readthedocs.io

License:

AGPL / AGPL-3.0-only

Recipe:

/r-scoper/meta.yaml

package r-scoper

Versions:

1.2.1-2,  1.2.1-1,  1.2.1-0,  1.2.0-0

Depends:

• libgcc-ng >=12

• libstdcxx-ng >=12

• r-alakazam >=1.2.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-doparallel

• r-dplyr >=1.0

• r-foreach

• r-ggplot2 >=3.3.4

• r-rcpp >=0.12.12

• r-rlang

• r-scales

• r-shazam >=1.1.0

• r-stringi

• r-tidyr >=1.0

Required By:

• r-enchantr

Installation

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

conda install r-scoper

and update with:

conda update r-scoper

or use the docker container:

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

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

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