Projects
My work in life science Sweden is quite varied with numerous different projects relating to everything from transcriptomics, pipeline development and statistics. While I cannot share details of on-going NBIS projects due to confidentiality agreements, I here list some of my Open Source projects and contributions.
Open Source projects
These are open source projects I have created and/or maintain:
- nf-core/spatialvi, a Nextflow/nf-core pipeline for analysing spatial transcriptomics data
- nf-core/rifseq, a Nextflow/nf-core pipeline for analysing the RIF-seq method for large-scale drug screening (currently not publicly available pending publication)
- seqCAT, an R/Bioconductor package for variant analysis and cell authentication using HTS data
- VarClust, a Python package for variant analyses of single-cell HTS data
- Tools for Reproducible Research, a course about working reproducibly in science and bioinformatics
- RNA-VC, a Snakemake pipeline for variant analyses of publicly available RNA-seq data
- nf-core/modules/quartonotebook, a Nextflow/nf-core module for rendering Quarto notebooks.
- A nf-core Quarto template following the nf-core visual identity and commonly used colours for rendering nf-core-themed reports
- simple-zoom.nvim, a simple plugin to add a Tmux-like zoom to Neovim
- slime-peek.nvim, a Neovim plugin for working with data exploration within R and Python
- conda-intel-env, a helper script for creating Intel-based Conda environments on MacOS ARM64
- docker-X11-interactive, a helper script for interactive plotting inside Docker containers on MacOS
- niri-run-or-raise, a run-or-raise-style script for the Niri window manager on Linux
- tmux-find-sessions, a fzf-powered helper script for listing and selecting Tmux sessions
Open Source contributions
These are open source projects I have contributed to:
- nf-core/scdownstream, a Nextflow/nf-core pipeline for running downstream analyses of single cell RNA-seq data
- nf-core/modules/spaceranger, a Nextflow/nf-core module for the 10x Genomics Space Ranger software.
- nf-core/test-datasets, a repository for storing test datasets used in nf-core pipelines and modules
- telekasten.nvim, a Neovim plugin for working with a markdown zettelkasten using
- Comment.nvim, a Neovim plugin for tree-sitter-supported commenting
- workflows-nextflow, a Software Carpentries lesson on Nextflow
