Objectives

The continuous developments of single-cell RNA-Seq (scRNA-Seq) have sparked an immense interest in understanding intercellular crosstalk. Multiple tools and resources that aid the investigation of cell-cell communication (CCC) were published recently. However, these methods and resources are usually in a fixed combination of a tool and its corresponding resource, but in principle any resource could be combined with any method.

LIANA Framework

To this end we built a framework to decouple the tools from their corresponding resources. In turn, we used the pipeline for the systematic comparison of all combinations between 15 resources and 6 tools.

landingpage

Tools

The tools implemented in this repository are:

  • CellPhoneDB algorithm (via Squidpy)
  • CellChat
  • NATMI
  • Connectome
  • SingleCellSignalR (SCA)
  • iTALK

Resources

Cell-cell Communication resources

The following CCC resources are accessible via this pipeline:

  • CellChatDB
  • CellPhoneDB
  • Ramilowski2015
  • Baccin2019
  • LRdb
  • Kiroauc2010
  • ICELLNET
  • iTALK
  • EMBRACE
  • HPMR
  • Guide2Pharma
  • connectomeDB2020
  • talklr
  • CellTalkDB
  • OmniPath

OmniPath

All the resources above are retrieved from OmniPath (https://omnipathdb.org/), and more specifically OmnipathR.

OmniPath itself is also a composite resource combining all the ones listed above. However the cell-cell interactions in OmniPath are more than simply the union of the ligand-receptor resources. OmniPath uses several further databases to collect information about the roles of proteins in intercellular communication and again other databases to find connections between them. At the same time, OmniPath blacklists certain wrong annotations, removing some of the contents of the original resources.

However the data of individual resources retrieved from the OmniPath web service is not affected by this, each resource supposed to be identical to its original form, apart from minor processing imperfections.

Reshuffled and Default Resources

Moreover, a Reshuffled (Random) resource can be generated via reshuffling any of the aforementioned using the BiRewire package, and each tool can be run with its ‘Default’ resource.

Install LIANA

LIANA uses CCC methods from both R and Python, as such dependencies for both need to be installed. LIANA is predominantly written in R and makes use of Seurat objects as input.

To install the LIANA framework run the following code in R:

library(devtools)  
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE) # ignore warning from iTALK 
devtools::BiocManager::install("ComplexHeatmap") # required for Connectome
install_github('saezlab/OmnipathR@ff3ad88e3915747e1b557bf44ac5396f9525dd7e') # install 4.0 version of OmnipathR

# install tools
devtools::install_github("sqjin/CellChat")  
devtools::install_github('msraredon/Connectome', ref = 'master')   
devtools::install_github("Coolgenome/iTALK", build_vignettes = TRUE)
# A modified version of SingleCellSignalR (SCA) that enables external resources
devtools::install_github(repo = "CostaLab/SingleCellSignalR_v1", subdir = "SingleCellSignalR")

# Finally, install LIANA
devtools::install_github('saezlab/liana')

Installation of all dependencies takes ~5-10 minutes.

Squidpy and NATMI are written in Python, as such a python environment with the prerequisites of these methods needs to be set up.

Please use the .yml file to set up a conda environment:

conda env create -f liana_env.yml

Note! NATMI and Squidpy are set by default to look for this conda environment (“liana_env”).

To use NATMI with LIANA, clone the lone modified NATMI repo into liana path by running the following in the terminal:

cd *insert fullpath*/liana
git clone https://github.com/saezlab/NATMI
Note that, NATMI was forked from its github repo and changed to be agnostic of the working directory when loading the resources.

If needed, use the following to locate the liana package

library(liana)
system.file(package = "liana")

Tutorial

See a tutorial how to use LIANA to run all methods and resource from above! The tutorial with the test data takes minutes to complete!

Citing LIANA:

Dimitrov, D., Türei, D., Boys, C., Nagai, J.S., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Dugourd, A., Valdeolivas, A. and Saez-Rodriguez, J., 2021. Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data. bioRxiv. 10.1101/2021.05.21.445160v1

Also, if you use the OmniPath CCC Resource for your analysis, please cite:

Türei, D., Valdeolivas, A., Gul, L., Palacio‐Escat, N., Klein, M., Ivanova, O., Ölbei, M., Gábor, A., Theis, F., Módos, D. and Korcsmáros, T., 2021. Integrated intra‐and intercellular signaling knowledge for multicellular omics analysis. Molecular systems biology, 17(3), p.e9923. https://doi.org/10.15252/msb.20209923

R session_info()

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       Ubuntu 20.04.2 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Berlin               
 date     2021-06-11                  

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date       lib source                               
 abind                  1.4-5      2016-07-21 [1] CRAN (R 4.0.2)                       
 annotate               1.68.0     2020-10-27 [1] Bioconductor                         
 AnnotationDbi          1.52.0     2020-10-27 [1] Bioconductor                         
 assertthat             0.2.1      2019-03-21 [1] CRAN (R 4.0.2)                       
 backports              1.2.1      2020-12-09 [1] CRAN (R 4.0.2)                       
 bbmle                  1.0.23.1   2020-02-03 [1] CRAN (R 4.0.3)                       
 bdsmatrix              1.3-4      2020-01-13 [1] CRAN (R 4.0.3)                       
 Biobase              * 2.50.0     2020-10-27 [1] Bioconductor                         
 BiocGenerics         * 0.36.0     2020-10-27 [1] Bioconductor                         
 BiocParallel           1.24.1     2020-11-06 [1] Bioconductor                         
 bit                    4.0.4      2020-08-04 [1] CRAN (R 4.0.2)                       
 bit64                  4.0.5      2020-08-30 [1] CRAN (R 4.0.2)                       
 bitops                 1.0-6      2013-08-17 [1] CRAN (R 4.0.2)                       
 blob                   1.2.1      2020-01-20 [1] CRAN (R 4.0.2)                       
 brew                   1.0-6      2011-04-13 [1] CRAN (R 4.0.2)                       
 cachem                 1.0.4      2021-02-13 [1] CRAN (R 4.0.3)                       
 Cairo                  1.5-12.2   2020-07-07 [1] CRAN (R 4.0.3)                       
 caTools                1.18.1     2021-01-11 [1] CRAN (R 4.0.3)                       
 CellChat               1.1.0      2021-05-02 [1] Github (sqjin/CellChat@b3ccf96)      
 cellranger             1.1.0      2016-07-27 [1] CRAN (R 4.0.2)                       
 checkmate              2.0.0      2020-02-06 [1] CRAN (R 4.0.3)                       
 circlize               0.4.12     2021-01-08 [1] CRAN (R 4.0.3)                       
 cli                    2.3.0      2021-01-31 [1] CRAN (R 4.0.3)                       
 clipr                  0.7.1      2020-10-08 [1] CRAN (R 4.0.2)                       
 clue                   0.3-58     2020-12-03 [1] CRAN (R 4.0.3)                       
 cluster                2.1.0      2019-06-19 [4] CRAN (R 4.0.0)                       
 coda                   0.19-4     2020-09-30 [1] CRAN (R 4.0.3)                       
 codetools              0.2-16     2018-12-24 [4] CRAN (R 4.0.0)                       
 colorspace             2.0-0      2020-11-11 [1] CRAN (R 4.0.2)                       
 combinat               0.0-8      2012-10-29 [1] CRAN (R 4.0.2)                       
 ComplexHeatmap         2.6.2      2020-11-12 [1] Bioconductor                         
 Connectome             1.0.1      2021-02-21 [1] Github (msraredon/Connectome@4531dd9)
 conquer                1.0.2      2020-08-27 [1] CRAN (R 4.0.2)                       
 cowplot                1.1.1      2020-12-30 [1] CRAN (R 4.0.3)                       
 crayon                 1.4.1      2021-02-08 [1] CRAN (R 4.0.3)                       
 curl                   4.3        2019-12-02 [1] CRAN (R 4.0.2)                       
 data.table             1.14.0     2021-02-21 [1] CRAN (R 4.0.3)                       
 DBI                    1.1.1      2021-01-15 [1] CRAN (R 4.0.3)                       
 DDRTree                0.1.5      2017-04-30 [1] CRAN (R 4.0.2)                       
 DelayedArray           0.16.1     2021-01-22 [1] Bioconductor                         
 deldir                 0.2-10     2021-02-16 [1] CRAN (R 4.0.3)                       
 densityClust           0.3        2017-10-24 [1] CRAN (R 4.0.2)                       
 desc                   1.2.0      2018-05-01 [1] CRAN (R 4.0.2)                       
 DESeq2                 1.30.1     2021-02-19 [1] Bioconductor                         
 DEsingle               1.10.0     2020-10-27 [1] Bioconductor                         
 digest                 0.6.27     2020-10-24 [1] CRAN (R 4.0.2)                       
 distillery             1.2        2020-11-21 [1] CRAN (R 4.0.3)                       
 docopt                 0.7.1      2020-06-24 [1] CRAN (R 4.0.2)                       
 doParallel             1.0.16     2020-10-16 [1] CRAN (R 4.0.2)                       
 dplyr                  1.0.4      2021-02-02 [1] CRAN (R 4.0.3)                       
 edgeR                  3.32.1     2021-01-14 [1] Bioconductor                         
 ellipsis               0.3.1      2020-05-15 [1] CRAN (R 4.0.2)                       
 evaluate               0.14       2019-05-28 [1] CRAN (R 4.0.2)                       
 extRemes               2.1        2020-11-24 [1] CRAN (R 4.0.3)                       
 fastICA                1.2-2      2019-07-08 [1] CRAN (R 4.0.2)                       
 fastmap                1.1.0      2021-01-25 [1] CRAN (R 4.0.3)                       
 fitdistrplus           1.1-3      2020-12-05 [1] CRAN (R 4.0.2)                       
 flexmix                2.3-17     2020-10-12 [1] CRAN (R 4.0.3)                       
 FNN                    1.1.3      2019-02-15 [1] CRAN (R 4.0.2)                       
 foreach                1.5.1      2020-10-15 [1] CRAN (R 4.0.2)                       
 future                 1.21.0     2020-12-10 [1] CRAN (R 4.0.2)                       
 future.apply           1.7.0      2021-01-04 [1] CRAN (R 4.0.3)                       
 gamlss                 5.2-0      2020-09-12 [1] CRAN (R 4.0.3)                       
 gamlss.data            5.1-4      2019-05-15 [1] CRAN (R 4.0.3)                       
 gamlss.dist            5.1-7      2020-07-13 [1] CRAN (R 4.0.3)                       
 genefilter             1.72.1     2021-01-21 [1] Bioconductor                         
 geneplotter            1.68.0     2020-10-27 [1] Bioconductor                         
 generics               0.1.0      2020-10-31 [1] CRAN (R 4.0.2)                       
 GenomeInfoDb           1.26.2     2020-12-08 [1] Bioconductor                         
 GenomeInfoDbData       1.2.4      2020-12-14 [1] Bioconductor                         
 GenomicRanges          1.42.0     2020-10-27 [1] Bioconductor                         
 GetoptLong             1.0.5      2020-12-15 [1] CRAN (R 4.0.3)                       
 gg.gap                 1.3        2019-09-30 [1] CRAN (R 4.0.3)                       
 ggalluvial             0.12.3     2020-12-05 [1] CRAN (R 4.0.3)                       
 ggplot2                3.3.3      2020-12-30 [1] CRAN (R 4.0.3)                       
 ggrepel                0.9.1      2021-01-15 [1] CRAN (R 4.0.3)                       
 ggridges               0.5.3      2021-01-08 [1] CRAN (R 4.0.3)                       
 GlobalOptions          0.1.2      2020-06-10 [1] CRAN (R 4.0.3)                       
 globals                0.14.0     2020-11-22 [1] CRAN (R 4.0.2)                       
 glue                   1.4.2      2020-08-27 [1] CRAN (R 4.0.2)                       
 goftest                1.2-2      2019-12-02 [1] CRAN (R 4.0.2)                       
 gplots                 3.1.1      2020-11-28 [1] CRAN (R 4.0.2)                       
 gridBase               0.4-7      2014-02-24 [1] CRAN (R 4.0.3)                       
 gridExtra              2.3        2017-09-09 [1] CRAN (R 4.0.2)                       
 gtable                 0.3.0      2019-03-25 [1] CRAN (R 4.0.2)                       
 gtools                 3.8.2      2020-03-31 [1] CRAN (R 4.0.2)                       
 hms                    1.0.0      2021-01-13 [1] CRAN (R 4.0.3)                       
 HSMMSingleCell         1.10.0     2020-10-29 [1] Bioconductor                         
 htmltools              0.5.1.1    2021-01-22 [1] CRAN (R 4.0.3)                       
 htmlwidgets            1.5.3      2020-12-10 [1] CRAN (R 4.0.2)                       
 httpuv                 1.5.5      2021-01-13 [1] CRAN (R 4.0.3)                       
 httr                   1.4.2      2020-07-20 [1] CRAN (R 4.0.2)                       
 ica                    1.0-2      2018-05-24 [1] CRAN (R 4.0.2)                       
 igraph                 1.2.6      2020-10-06 [1] CRAN (R 4.0.2)                       
 IRanges                2.24.1     2020-12-12 [1] Bioconductor                         
 irlba                  2.3.3      2019-02-05 [1] CRAN (R 4.0.2)                       
 iTALK                  0.1.0      2021-02-21 [1] Github (Coolgenome/iTALK@6d9b390)    
 iterators              1.0.13     2020-10-15 [1] CRAN (R 4.0.2)                       
 jsonlite               1.7.2      2020-12-09 [1] CRAN (R 4.0.2)                       
 KernSmooth             2.23-17    2020-04-26 [4] CRAN (R 4.0.0)                       
 knitr                  1.31       2021-01-27 [1] CRAN (R 4.0.3)                       
 later                  1.1.0.1    2020-06-05 [1] CRAN (R 4.0.2)                       
 lattice                0.20-41    2020-04-02 [4] CRAN (R 4.0.0)                       
 lazyeval               0.2.2      2019-03-15 [1] CRAN (R 4.0.2)                       
 leiden                 0.3.7      2021-01-26 [1] CRAN (R 4.0.3)                       
 liana                * 0.0.1      2021-06-11 [1] local                                
 lifecycle              1.0.0      2021-02-15 [1] CRAN (R 4.0.3)                       
 limma                  3.46.0     2020-10-27 [1] Bioconductor                         
 listenv                0.8.0      2019-12-05 [1] CRAN (R 4.0.2)                       
 Lmoments               1.3-1      2019-03-15 [1] CRAN (R 4.0.3)                       
 lmtest                 0.9-38     2020-09-09 [1] CRAN (R 4.0.2)                       
 locfit                 1.5-9.4    2020-03-25 [1] CRAN (R 4.0.2)                       
 logger                 0.2.0      2021-03-04 [1] CRAN (R 4.0.3)                       
 magrittr               2.0.1      2020-11-17 [1] CRAN (R 4.0.2)                       
 MASS                   7.3-53     2020-09-09 [4] CRAN (R 4.0.2)                       
 MAST                   1.16.0     2020-10-27 [1] Bioconductor                         
 Matrix                 1.2-18     2019-11-27 [4] CRAN (R 4.0.0)                       
 MatrixGenerics         1.2.1      2021-01-30 [1] Bioconductor                         
 MatrixModels           0.4-1      2015-08-22 [1] CRAN (R 4.0.2)                       
 matrixStats            0.58.0     2021-01-29 [1] CRAN (R 4.0.3)                       
 maxLik                 1.4-6      2020-11-24 [1] CRAN (R 4.0.3)                       
 memoise                2.0.0      2021-01-26 [1] CRAN (R 4.0.3)                       
 mgcv                   1.8-33     2020-08-27 [4] CRAN (R 4.0.2)                       
 mime                   0.10       2021-02-13 [1] CRAN (R 4.0.3)                       
 miniUI                 0.1.1.1    2018-05-18 [1] CRAN (R 4.0.2)                       
 miscTools              0.6-26     2019-12-08 [1] CRAN (R 4.0.3)                       
 modeltools             0.2-23     2020-03-05 [1] CRAN (R 4.0.3)                       
 monocle                2.18.0     2020-10-27 [1] Bioconductor                         
 multtest               2.46.0     2020-10-27 [1] Bioconductor                         
 munsell                0.5.0      2018-06-12 [1] CRAN (R 4.0.2)                       
 mvtnorm                1.1-1      2020-06-09 [1] CRAN (R 4.0.2)                       
 network                1.16.1     2020-10-07 [1] CRAN (R 4.0.2)                       
 nlme                   3.1-149    2020-08-23 [4] CRAN (R 4.0.2)                       
 NMF                    0.23.0     2020-08-01 [1] CRAN (R 4.0.3)                       
 nnet                   7.3-14     2020-04-26 [4] CRAN (R 4.0.0)                       
 numDeriv               2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.3)                       
 OmnipathR              2.99.18    2021-06-09 [1] Github (saezlab/OmnipathR@ff3ad88)   
 parallelly             1.24.0     2021-03-14 [1] CRAN (R 4.0.3)                       
 patchwork              1.1.1      2020-12-17 [1] CRAN (R 4.0.3)                       
 pbapply                1.4-3      2020-08-18 [1] CRAN (R 4.0.2)                       
 pcaMethods             1.82.0     2020-10-27 [1] Bioconductor                         
 pheatmap               1.0.12     2019-01-04 [1] CRAN (R 4.0.2)                       
 pillar                 1.4.7      2020-11-20 [1] CRAN (R 4.0.2)                       
 pkgconfig              2.0.3      2019-09-22 [1] CRAN (R 4.0.2)                       
 pkgload                1.1.0      2020-05-29 [1] CRAN (R 4.0.2)                       
 pkgmaker               0.32.2     2020-10-20 [1] CRAN (R 4.0.3)                       
 plotly                 4.9.3      2021-01-10 [1] CRAN (R 4.0.3)                       
 plyr                   1.8.6      2020-03-03 [1] CRAN (R 4.0.2)                       
 png                    0.1-7      2013-12-03 [1] CRAN (R 4.0.2)                       
 polyclip               1.10-0     2019-03-14 [1] CRAN (R 4.0.2)                       
 pracma                 2.3.3      2021-01-23 [1] CRAN (R 4.0.3)                       
 prettyunits            1.1.1      2020-01-24 [1] CRAN (R 4.0.2)                       
 progress               1.2.2      2019-05-16 [1] CRAN (R 4.0.2)                       
 promises               1.2.0.1    2021-02-11 [1] CRAN (R 4.0.3)                       
 pscl                   1.5.5      2020-03-07 [1] CRAN (R 4.0.3)                       
 purrr                * 0.3.4      2020-04-17 [1] CRAN (R 4.0.2)                       
 qlcMatrix              0.9.7      2018-04-20 [1] CRAN (R 4.0.2)                       
 quantreg               5.83       2021-01-22 [1] CRAN (R 4.0.3)                       
 R6                     2.5.0      2020-10-28 [1] CRAN (R 4.0.2)                       
 randomcoloR            1.1.0.1    2019-11-24 [1] CRAN (R 4.0.3)                       
 RANN                   2.6.1      2019-01-08 [1] CRAN (R 4.0.2)                       
 rappdirs               0.3.3      2021-01-31 [1] CRAN (R 4.0.3)                       
 RColorBrewer           1.1-2      2014-12-07 [1] CRAN (R 4.0.2)                       
 Rcpp                   1.0.6      2021-01-15 [1] CRAN (R 4.0.3)                       
 RcppAnnoy              0.0.18     2020-12-15 [1] CRAN (R 4.0.3)                       
 RcppArmadillo          0.10.2.1.0 2021-02-09 [1] CRAN (R 4.0.3)                       
 RCurl                  1.98-1.3   2021-03-16 [1] CRAN (R 4.0.3)                       
 readr                  1.4.0      2020-10-05 [1] CRAN (R 4.0.2)                       
 readxl                 1.3.1      2019-03-13 [1] CRAN (R 4.0.2)                       
 registry               0.5-1      2019-03-05 [1] CRAN (R 4.0.3)                       
 reshape2               1.4.4      2020-04-09 [1] CRAN (R 4.0.2)                       
 reticulate             1.18       2020-10-25 [1] CRAN (R 4.0.2)                       
 rjson                  0.2.20     2018-06-08 [1] CRAN (R 4.0.3)                       
 rlang                  0.4.10     2020-12-30 [1] CRAN (R 4.0.3)                       
 rle                    0.9.2      2020-09-25 [1] CRAN (R 4.0.3)                       
 rmarkdown              2.7        2021-02-19 [1] CRAN (R 4.0.3)                       
 RMTstat                0.3        2014-11-01 [1] CRAN (R 4.0.3)                       
 rngtools               1.5        2020-01-23 [1] CRAN (R 4.0.2)                       
 ROCR                   1.0-11     2020-05-02 [1] CRAN (R 4.0.2)                       
 Rook                   1.1-1      2014-10-20 [1] CRAN (R 4.0.3)                       
 rpart                  4.1-15     2019-04-12 [4] CRAN (R 4.0.0)                       
 rprojroot              2.0.2      2020-11-15 [1] CRAN (R 4.0.2)                       
 RSpectra               0.16-0     2019-12-01 [1] CRAN (R 4.0.2)                       
 RSQLite                2.2.3      2021-01-24 [1] CRAN (R 4.0.3)                       
 rsvd                   1.0.3      2020-02-17 [1] CRAN (R 4.0.2)                       
 Rtsne                  0.15       2018-11-10 [1] CRAN (R 4.0.2)                       
 S4Vectors              0.28.1     2020-12-09 [1] Bioconductor                         
 sandwich               3.0-0      2020-10-02 [1] CRAN (R 4.0.2)                       
 scales                 1.1.1      2020-05-11 [1] CRAN (R 4.0.2)                       
 SCAomni                0.0.1.8    2021-02-21 [1] Bioconductor                         
 scattermore            0.7        2020-11-24 [1] CRAN (R 4.0.3)                       
 scde                   2.18.0     2020-10-27 [1] Bioconductor                         
 sctransform            0.3.2      2020-12-16 [1] CRAN (R 4.0.3)                       
 sessioninfo            1.1.1      2018-11-05 [1] CRAN (R 4.0.2)                       
 Seurat                 3.2.3      2020-12-15 [1] CRAN (R 4.0.3)                       
 shape                  1.4.5      2020-09-13 [1] CRAN (R 4.0.3)                       
 shiny                  1.6.0      2021-01-25 [1] CRAN (R 4.0.3)                       
 SIMLR                  1.16.0     2020-10-27 [1] Bioconductor                         
 SingleCellExperiment   1.12.0     2020-10-27 [1] Bioconductor                         
 slam                   0.1-48     2020-12-03 [1] CRAN (R 4.0.2)                       
 sna                    2.6        2020-10-06 [1] CRAN (R 4.0.3)                       
 SparseM                1.81       2021-02-18 [1] CRAN (R 4.0.3)                       
 sparsesvd              0.2        2019-07-15 [1] CRAN (R 4.0.2)                       
 spatstat               1.64-1     2020-05-12 [1] CRAN (R 4.0.2)                       
 spatstat.data          2.1-0      2021-03-21 [1] CRAN (R 4.0.3)                       
 spatstat.utils         2.1-0      2021-03-15 [1] CRAN (R 4.0.3)                       
 statnet.common         4.4.1      2020-10-03 [1] CRAN (R 4.0.3)                       
 stringi                1.5.3      2020-09-09 [1] CRAN (R 4.0.2)                       
 stringr                1.4.0      2019-02-10 [1] CRAN (R 4.0.2)                       
 SummarizedExperiment   1.20.0     2020-10-27 [1] Bioconductor                         
 survival               3.2-7      2020-09-28 [1] CRAN (R 4.0.2)                       
 svglite                2.0.0      2021-02-20 [1] CRAN (R 4.0.3)                       
 systemfonts            1.0.1      2021-02-09 [1] CRAN (R 4.0.3)                       
 tensor                 1.5        2012-05-05 [1] CRAN (R 4.0.2)                       
 testthat             * 3.0.2      2021-02-14 [1] CRAN (R 4.0.3)                       
 tibble               * 3.0.6      2021-01-29 [1] CRAN (R 4.0.3)                       
 tidyr                  1.1.2      2020-08-27 [1] CRAN (R 4.0.2)                       
 tidyselect             1.1.0      2020-05-11 [1] CRAN (R 4.0.2)                       
 uwot                   0.1.10     2020-12-15 [1] CRAN (R 4.0.3)                       
 V8                     3.4.0      2020-11-04 [1] CRAN (R 4.0.3)                       
 vctrs                  0.3.6      2020-12-17 [1] CRAN (R 4.0.3)                       
 VGAM                   1.1-5      2021-01-14 [1] CRAN (R 4.0.3)                       
 viridis                0.5.1      2018-03-29 [1] CRAN (R 4.0.2)                       
 viridisLite            0.3.0      2018-02-01 [1] CRAN (R 4.0.2)                       
 withr                  2.4.1      2021-01-26 [1] CRAN (R 4.0.3)                       
 xfun                   0.21       2021-02-10 [1] CRAN (R 4.0.3)                       
 XML                    3.99-0.5   2020-07-23 [1] CRAN (R 4.0.2)                       
 xml2                   1.3.2      2020-04-23 [1] CRAN (R 4.0.2)                       
 xtable                 1.8-4      2019-04-21 [1] CRAN (R 4.0.2)                       
 XVector                0.30.0     2020-10-27 [1] Bioconductor                         
 yaml                   2.2.1      2020-02-01 [1] CRAN (R 4.0.2)                       
 zlibbioc               1.36.0     2020-10-27 [1] Bioconductor                         
 zoo                    1.8-8      2020-05-02 [1] CRAN (R 4.0.2)                       

[1] /home/dbdimitrov/R/x86_64-pc-linux-gnu-library/4.0
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library