multideconv is an integrative pipeline for combining
first- and second-generation cell type deconvolution methods from bulk
RNA-seq data, as described in Hurtado
et al., 2025.
Installation
To avoid GitHub API rate limit issues, set up a Personal Access Token (PAT) before installing:
# install.packages(c("usethis", "gitcreds"))
usethis::create_github_token()
gitcreds::gitcreds_set()Install multideconv from GitHub:
# install.packages("pak")
pak::pkg_install("VeraPancaldiLab/multideconv")Tutorials
Step-by-step tutorials are available in the Articles section of the navigation bar:
- Deconvolution with default methods — run first-generation deconvolution and access built-in signatures
- Single-cell deconvolution — construct metacells and apply second-generation methods
- Pseudo-bulk profiles and benchmarking — create pseudo-bulk data, generate custom signatures, and benchmark performance
- Cell type subgroup analysis — derive cell-type subgroups and build a deconvolution dictionary
- Machine learning workflows — use subgroup features in cross-validated ML models
Citation
If you use multideconv in a scientific publication,
please cite:
Hurtado, M., Essabbar, A., Khajavi, L., & Pancaldi, V. (2025). multideconv – Integrative pipeline for cell type deconvolution from bulk RNAseq using first and second generation methods. bioRxiv. https://doi.org/10.1101/2025.04.29.651220