immunedeconv: An R repository from omnideconv

an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.

Basic usage

Deconvolution of human data:

immunedeconv::deconvolute(gene_expression_matrix, "quantiseq")

Deconvolution of mouse data:

immunedeconv::deconvolute_mouse(gene_expression_matrix, "mmcp_counter")

where gene_expression_matrix is a matrix with genes in rows and samples in columns. The rownames must be HGNC symbols for human data, or MGI gene symbols for mouse data. The colnames must be sample names. For human data, the method can be one of

quantiseq
timer
cibersort
cibersort_abs
mcp_counter
xcell
epic
abis
consensus_tme
estimate

The ESTIMATE algorithm, which computes a score for the tumoral, immune and stromal components and the fraction of tumor purity of a sample, has been implemented.

immunedeconv::deconvolute_estimate(gene_expression_matrix)

The methods available for the deconvolution of mouse data are

mmcp_counter
seqimmucc
dcq
base

In addition, human-based methods can be used to deconvolute mouse data through the conversion to orthologous gene names

gene_expression_matrix <- immunedeconv::mouse_genes_to_human(gene_expression_matrix)
immunedeconv::deconvolute(gene_expression_matrix, "quantiseq")

Finally, certain methods can be used with custom signatures, consisting of either a signature matrix or signature genes for the cell types of interest. Since the information used to deconvolute the bulk is user-provided, these functions can be used for different tissues and organisms. The functions may require different input data formats, related to the requirements of each method. Please refer to their documentation. The available methods are

base:  deconvolute_base_custom()
cibersort norm/abs:  deconvolute_cibersort_custom()
epic: deconvolute_epic_custom()
consensus_tme: deconvolute_consensus_tme_custom()

For more detailed usage instructions, see the Documentation:

Available methods, Licenses, Citations

Note that, while immunedeconv itself is free (BSD), you may need to obtain a license to use the individual methods. See the table below for more information. If you use this package in your work, please cite both our package and the method(s) you are using.

Sturm, G., Finotello, F., Petitprez, F., Zhang, J. D., Baumbach, J., Fridman, W. H., ..., List, M., Aneichyk, T. (2019). Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Bioinformatics, 35(14), i436-i445. https://doi.org/10.1093/bioinformatics/btz363

method	organism	license	citation
quanTIseq	human	free (BSD)	Finotello, F., Mayer, C., Plattner, C., Laschober, G., Rieder, D., Hackl, H., ..., Sopper, S. (2019). Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome medicine, 11(1), 34. https://doi.org/10.1186/s13073-019-0638-6
TIMER	human	free (GPL 2.0)	Li, B., Severson, E., Pignon, J.-C., Zhao, H., Li, T., Novak, J., … Liu, X. S. (2016). Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biology, 17(1), 174. https://doi.org/10.1186/s13059-016-1028-7
CIBERSORT	human	free for non-commerical use only	Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., … Alizadeh, A. A. (2015). Robust enumeration of cell subsets from tissue expression profiles. Nature Methods, 12(5), 453–457. https://doi.org/10.1038/nmeth.3337
MCPCounter	human	free (GPL 3.0)	Becht, E., Giraldo, N. A., Lacroix, L., Buttard, B., Elarouci, N., Petitprez, F., … de Reyniès, A. (2016). Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biology, 17(1), 218. https://doi.org/10.1186/s13059-016-1070-5
xCell	human	free (GPL 3.0)	Aran, D., Hu, Z., & Butte, A. J. (2017). xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biology, 18(1), 220. https://doi.org/10.1186/s13059-017-1349-1
EPIC	human	free for non-commercial use only (Academic License)	Racle, J., de Jonge, K., Baumgaertner, P., Speiser, D. E., & Gfeller, D. (2017). Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. ELife, 6, e26476. https://doi.org/10.7554/eLife.26476
ESTIMATE	human	free (GPL 2.0)	Yoshihara, K., Shahmoradgoli, M., Martínez, E., Vegesna, R., Kim, H., Torres-Garcia, W., Treviño, V., Shen, H., Laird, P. W., Levine, D. A., Carter, S. L., Getz, G., Stemke-Hale, K., Mills, G. B., & Verhaak, R. G. (2013). Inferring tumour purity and stromal and immune cell admixture from expression data. Nature communications, 4, 2612. https://doi.org/10.1038/ncomms3612
ABIS	human	free (GPL 2.0)	Monaco, G., Lee, B., Xu, W., Mustafah, S., Hwang, Y. Y., ..., Larbi, A. (2019). RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types. Cell reports, 26(6), 1627–1640.e7. https://doi.org/10.1016/j.celrep.2019.01.041
ConsensusTME	human	free (GPL 3.0)	Jiménez-Sánchez, A., Cast, O., & Miller, M. L. (2019). Comprehensive Benchmarking and Integration of Tumor Microenvironment Cell Estimation Methods. Cancer research, 79(24), 6238–6246. https://doi.org/10.1158/0008-5472.CAN-18-3560
mMCPCounter	mouse	free (GPL 3.0)	Petitprez, F., Levy, S., Sun, C. M., Meylan, M., ..., de Reyniès, A. (2020). The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression. Genome medicine, 12(1), 86. https://doi.org/10.1186/s13073-020-00783-w
seqImmuCC	mouse	free for non-commerical use only	Chen, Z., Quan, L., Huang, A., Zhao, Q., Yuan, Y., Yuan, X., ..., Wu, A. (2018). seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data. Frontiers in immunology, 9, 1286. https://doi.org/10.3389/fimmu.2018.01286
DCQ	mouse	free (GPL 2.0)	Altboum, Z., Steuerman, Y., David, E., Barnett-Itzhaki, Z., Valadarsky, L., ..., Amit, I. (2014). Digital cell quantification identifies global immune cell dynamics during influenza infection. Molecular systems biology, 10(2), 720. https://doi.org/10.1002/msb.134947
BASE	mouse	free	Varn, F. S., Andrews, E. H., Mullins, D. W., & Cheng, C. (2016). Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles. Nature communications, 7, 10248. https://doi.org/10.1038/ncomms10248

Comparison of the methods

For a benchmark comparison of the human-based methods, please see our publication. If you would like to benchmark additional methods, please see our benchmark pipeline.

Installation

System requirements: R >= 4.1. Only linux is officially supported, but Mac/Windows should work, too.

Bioconda (Linux/MacOS only)

The easiest way to retrieve this package and all its dependencies is to use Anaconda. The installation typically completes within minutes.

Download Miniconda, if you don't have a conda installation already.
(Optional) create and activate an environment for deconvolution:

conda create -n deconvolution
conda activate deconvolution

Install the immunedeconv package

conda install -c bioconda -c conda-forge r-immunedeconv

conda will automatically install the package and all dependencies. You can then open an R instance within the environment and use the package.

Standard R Package

We highly recommend using conda, as it will avoid incompatibilities between different package versions. That being said, you can also install immunedeconv as a regular R package in your default R installation. The installation typically completes within 30 minutes, depending on how many dependency packages need to be compiled.

The easiest way to do so is to use the remotes package, which will automatically download all CRAN, Bioconductor and GitHub dependencies:

install.packages("remotes")
remotes::install_github("omnideconv/immunedeconv")

Credits

This package was originally developed by Gregor Sturm in 2018 at Pieris Pharmaceuticals GmbH in collaboration with Markus List, Tatsiana Aneichyk, and Francesca Finotello. Gregor Sturm continued to support this package while at ICBI (Med Uni Innsbruck). In 2022, this repository moved to the omnideconv organization, a joint effort of the List Lab and Finotello Lab dedicated to improve accessibility of deconvolution methods. At this point Lorenzo Merotto became primary maintainer of the immunedeconv package.