Package: sc-dandelion
Hi there! I have put together a python package for analyzing single cell BCR/TCR data from 10x Genomics 5' solution! It streamlines the pre-processing, leveraging some tools from immcantation suite, and integrates with scanpy/anndata for single-cell BCR/TCR analysis. It also includes a couple of functions for visualization.Citationdandelionis now published atNature Biotechnology!Please cite the following if you use version 0.3.0 onwards:Suo, C., Polanski, K., Dann, E. et al.Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins. Nat Biotechnol (2023).https://doi.org/10.1038/s41587-023-01734-7dandelionwas originally published atNature Medicine:Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis CS Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W Mather, Rik GH Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina CD Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M Janes, Claire M Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Y Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolic, Christopher JA Duncan, Ken Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Gottgens, Muzlifah Haniffa.Single-cell multi-omics analysis of the immune response in COVID-19.Nature Medicine 2021.04.20; doi:https://dx.doi.org/10.1038/s41591-021-01329-2OverviewIllustration of theDandelionclass slotsPlease refer to thedocumentation.The raw files for the examples can be downloaded from 10X's Single Cell Immune Profiling datasetswebsite.InstallationSingularity containerdandelionnow comes ready in the form of a singularity container:singularitypulllibrary://kt16/default/sc-dandelion:latest
singularityshell--writable-tmpfs-B$PWDsc-dandelion_latest.sifThis will load up a container that has all the required dependencies installed.This can be used for the preprocessing steps by navigating to the data folder and use:singularityrun-B$PWDsc-dandelion_latest.sifdandelion-preprocessIf you have multiple samples to process, it is reccomended to specify the--metaoption with a.csvfile detailing the samples:singularityrun-B$PWDsc-dandelion_latest.sifdandelion-preprocess--metameta.csvPython packageStart off by creating a conda environment containing scanpy, followingofficial scanpy instructions. Once done, run the following:condainstall-cconda-forgegraph-tool
pipinstallsc-dandelionBetween this and the pipelines within the singularity container, you should be covered for most of your needs.Basic requirementsPython packages# condapython>=3.7(conda-forge)numpy>=1.18.4(conda-forge)pandas>=1.0.3(conda-forge)distance>=0.1.3(conda-forge)jupyter(conda-forge)# if running via a notebookscikit-learn>=0.23.0(conda-forge)numba>=0.48.0(conda-forge)pytables>=3.6.1(conda-forge)seaborn>=0.10.1(conda-forge)leidenalg>=0.8.0(conda-forge)plotnine>=0.6.0(conda-forge)graph-tool>=2.3.5(conda-forge)# optional# Other executables (through conda)blast>=2.10.1(bioconda)igblast>=1.15.0(bioconda)# pipanndata>=0.7.1scanpy>=1.4.6scrublet>=0.2.1changeo>=1.0.0presto>=0.6.0polyleven>=0.5networkx>=2.4rpy2>=3.4.2AcknowledgementsI would like to acknowledge the contributions from Dr. Chenqu Suo, Dr. Krysztof Polanksi, Dr. Sarah Teichmann and Prof. Menna Clatworthy, who helped with the initial conception of the project and for all discussions.I would also like to acknowledge Dr. Ondrej Suschanek, Dr. Benjamin Stewart, Dr. Rachel Bashford-Rogers, Dr. Jongeun Park,  Dr. Cecilia-Dominguez Conde, Dr. Kirsten Stewart, Dr. Hamish King and Dr. Peng He with whom I have had very useful discussions. I would also like to thank my wife who helped name the package, because she thought the plots looked like a dandelion =D.SupportSupport is provided on a voluntary basis, as time permits.If there are any ideas, comments, suggestions, thing you would like to know more etc., please feel free to email me atz.tuong@uq.edu.auor post in the issue tracker and I will get back to you.