The R package RNAseqNet can be used to
infer networks from RNA-seq expression data. The count data are given as
a \(n \times p\) matrix in which \(n\) is the number of individuals and \(p\) the number of genes. This matrix is
denoted by \(\mathbf{X}\) in the
sequel.
Eventually, the RNA-seq dataset is complemented with an \(n' \times d\) matrix, \(\mathbf{Y}\) which can be used to impute missing individuals in \(\mathbf{X}\) as described in [Imbert et al., 2018].
The RNAseqNet User’s Guide can be opened with:
The location of the source file is given by:
Imbert, A., Valsesia, A., Le Gall, C., Armenise, C., Lefebvre, G., Gourraud, P.A., Viguerie, N. and Villa-Vialaneix, N. (2018) Multiple hot-deck imputation for network inference from RNA sequencing data. Bioinformatics. DOI: http://dx.doi.org/10.1093/bioinformatics/btx819.
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.39 R6_2.6.1 fastmap_1.2.0 xfun_0.59
## [5] maketools_1.3.2 cachem_1.1.0 knitr_1.51 htmltools_0.5.9
## [9] rmarkdown_2.31 buildtools_1.0.0 lifecycle_1.0.5 cli_3.6.6
## [13] sass_0.4.10 jquerylib_0.1.4 compiler_4.6.1 sys_3.4.3
## [17] tools_4.6.1 evaluate_1.0.5 bslib_0.11.0 yaml_2.3.12
## [21] jsonlite_2.0.0 rlang_1.2.0