bngal creates co-occurrence networks from microbial taxonomic abundance data.
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bngal is a software package developed to create co-occurrence networks from microbial taxonomic abundance data. bngal is written in the R programming language as a standalone package as well as a command-line utility. These images are functional containers for the bngal-cli commands bngal-build-nets and bngal-summarize-nets based on tagged GitHub releases. Note that these containers expect your input data to be mounted into the /work directory. See the Wiki page for more information.
# define input files
ASV_TABLE=example-asv-table.csv
META_DATA=example-metadata.csv
# define output directory
OUT_DR=`pwd`/all-communities
mkdir -p $OUT_DR
# using Docker
docker run -v `pwd`:/work -it mjsel/bngal:1.0.0 \
bngal-build-nets \
--asv_table=${ASV_TABLE} \
--metadata=${META_DATA} \
--output=${OUT_DR}
docker run -v `pwd`:/work -it mjsel/bngal:1.0.0 \
bngal-summarize-nets \
--asv_table=${ASV_TABLE} \
--metadata=${META_DATA} \
--network_dir=${OUT_DR} \
--fill_ebc_by="metadata_var_you_want_to_visualize"
Content type
Image
Digest
sha256:b0fade259…
Size
2.1 GB
Last updated
8 months ago
docker pull mjsel/bngal:1.0.0