A docker container with tools to help analyze Immune Repertoire from (currently bulk) RNAseq.
Currently MiXCR (https://github.com/milaboratory/mixcr), Immunarch (https://immunarch.com/) and some components of the Imcantation framework (https://immcantation.readthedocs.io/) are added. Development is still in progress.
This is a container designed to be used as part of a Nextflow pipeline. Additionally, nextflow can also be run inside the contatiner, although this is recommended for testing purposes only.
If the measured data is in the input_data folder of the current directory (alternatively, using test data in test_datas/imulated_input), a basic report can be generated issuing the following command:
docker run -it -v $PWD:/home/rstudio/local_files \
szabogtamas/repertoireseq \
nextflow run /home/rstudio/repo_files/nextflow/main.nf \
--input_folder /home/rstudio/local_files/input_data \
--clonotype_dir /home/rstudio/local_files/report/reconstruction_logs \
--table_path /home/rstudio/local_files/report/repertoire_summary.xlsx \
--figure_path /home/rstudio/local_files/report/figures \
--report_folder /home/rstudio/local_files/report \
--report_filename "my_test_repertoire_report.html" \
--report_title "A test report" \
--report_author "Label" \
--condition_order "Control,Anergic,Reacting" \
--report_author "Me"
In addition to the generated interactive html report, some major figures will also be exported in pdf format, to the figures folder. Assembly reports and a raw repertoire table will also be generated.
The range of figures generated by the notebook template, includes some very basic decriptive stats, like clonotype abundance:
As welll as some slightly more complex representations, like convergence of clones.
A simulated dataset, derived from Ig sequences published by Goldstein et al. is available in test_data/simulated_input folder.