+sessionInfo() +#> R version 4.4.1 (2024-06-14) +#> Platform: x86_64-pc-linux-gnu +#> Running under: Ubuntu 22.04.4 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-r0.3.20.so; LAPACK version 3.10.0 +#> +#> locale: +#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 +#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 +#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C +#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C +#> +#> time zone: UTC +#> tzcode source: system (glibc) +#> +#> attached base packages: +#> [1] stats graphics grDevices utils datasets methods base +#> +#> other attached packages: +#> [1] MSstatsBioNet_0.99.0 +#> +#> loaded via a namespace (and not attached): +#> [1] base64url_1.4 jsonlite_1.8.8 compiler_4.4.1 +#> [4] crayon_1.5.3 gtools_3.9.5 IRdisplay_1.1 +#> [7] bitops_1.0-7 RCy3_2.24.0 jquerylib_0.1.4 +#> [10] systemfonts_1.1.0 textshaping_0.4.0 uuid_1.2-0 +#> [13] yaml_2.3.9 fastmap_1.2.0 IRkernel_1.3.2 +#> [16] R6_2.5.1 knitr_1.48 backports_1.5.0 +#> [19] BiocGenerics_0.50.0 graph_1.82.0 XML_3.99-0.17 +#> [22] desc_1.4.3 bslib_0.7.0 pillar_1.9.0 +#> [25] RColorBrewer_1.1-3 rlang_1.1.4 utf8_1.2.4 +#> [28] cachem_1.1.0 stringi_1.8.4 repr_1.1.7 +#> [31] xfun_0.46 caTools_1.18.2 fs_1.6.4 +#> [34] sass_0.4.9 RJSONIO_1.3-1.9 cli_3.6.3 +#> [37] pkgdown_2.1.0 digest_0.6.36 base64enc_0.1-3 +#> [40] pbdZMQ_0.3-11 lifecycle_1.0.4 r2r_0.1.1 +#> [43] vctrs_0.6.5 KernSmooth_2.23-24 evaluate_0.24.0 +#> [46] glue_1.7.0 ragg_1.3.2 stats4_4.4.1 +#> [49] RCurl_1.98-1.16 fansi_1.0.6 rmarkdown_2.27 +#> [52] httr_1.4.7 gplots_3.1.3.1 tools_4.4.1 +#> [55] htmltools_0.5.8.1
sessionInfo() +#> R version 4.4.1 (2024-06-14) +#> Platform: x86_64-pc-linux-gnu +#> Running under: Ubuntu 22.04.4 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-r0.3.20.so; LAPACK version 3.10.0 +#> +#> locale: +#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 +#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 +#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C +#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C +#> +#> time zone: UTC +#> tzcode source: system (glibc) +#> +#> attached base packages: +#> [1] stats graphics grDevices utils datasets methods base +#> +#> other attached packages: +#> [1] MSstatsBioNet_0.99.0 +#> +#> loaded via a namespace (and not attached): +#> [1] base64url_1.4 jsonlite_1.8.8 compiler_4.4.1 +#> [4] crayon_1.5.3 gtools_3.9.5 IRdisplay_1.1 +#> [7] bitops_1.0-7 RCy3_2.24.0 jquerylib_0.1.4 +#> [10] systemfonts_1.1.0 textshaping_0.4.0 uuid_1.2-0 +#> [13] yaml_2.3.9 fastmap_1.2.0 IRkernel_1.3.2 +#> [16] R6_2.5.1 knitr_1.48 backports_1.5.0 +#> [19] BiocGenerics_0.50.0 graph_1.82.0 XML_3.99-0.17 +#> [22] desc_1.4.3 bslib_0.7.0 pillar_1.9.0 +#> [25] RColorBrewer_1.1-3 rlang_1.1.4 utf8_1.2.4 +#> [28] cachem_1.1.0 stringi_1.8.4 repr_1.1.7 +#> [31] xfun_0.46 caTools_1.18.2 fs_1.6.4 +#> [34] sass_0.4.9 RJSONIO_1.3-1.9 cli_3.6.3 +#> [37] pkgdown_2.1.0 digest_0.6.36 base64enc_0.1-3 +#> [40] pbdZMQ_0.3-11 lifecycle_1.0.4 r2r_0.1.1 +#> [43] vctrs_0.6.5 KernSmooth_2.23-24 evaluate_0.24.0 +#> [46] glue_1.7.0 ragg_1.3.2 stats4_4.4.1 +#> [49] RCurl_1.98-1.16 fansi_1.0.6 rmarkdown_2.27 +#> [52] httr_1.4.7 gplots_3.1.3.1 tools_4.4.1 +#> [55] htmltools_0.5.8.1
Wu A, Vitek O (2024). -MSstatsBioNet: Protein-Protein Interaction Analysis for MS-based Proteomics Experiments. -R package version 0.1.0, https://vitek-lab.github.io/MSstatsBioNet/, http://msstats.org. +MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments. +R package version 0.99.0, https://vitek-lab.github.io/MSstatsBioNet/, http://msstats.org.
@Manual{, - title = {MSstatsBioNet: Protein-Protein Interaction Analysis for MS-based Proteomics Experiments}, + title = {MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments}, author = {Anthony Wu and Olga Vitek}, year = {2024}, - note = {R package version 0.1.0, https://vitek-lab.github.io/MSstatsBioNet/}, + note = {R package version 0.99.0, https://vitek-lab.github.io/MSstatsBioNet/}, url = {http://msstats.org}, }
This package provides a suite of functions to query various network databases, filter queries & results, and visualize networks.
To install this package on bioconductor, run the following command:
if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +BiocManager::install("MSstatsBioNet")
You can install the development version of this package through Github:
devtools::install_github("Vitek-Lab/MSstatsConvert", build_vignettes = TRUE)
getSubnetworkFromIndra
visualizeNetworks
NEWS.md