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ReporterScore

library(ReporterScore)

‘ReporterScore’

Generalized Reporter Score-based Enrichment Analysis for Omics Data

Citation

To cite ‘ReporterScore’ in publications use:

C. Peng, Q. Chen, S. Tan, X. Shen, C. Jiang, Generalized Reporter Score-based Enrichment Analysis for Omics Data. Briefings in Bioinformatics (2024). https://doi.org/10.1093/bib/bbae116.

Please go to https://github.com/Asa12138/ReporterScore for more details.

Install

if (!require("devtools")) install.packages("devtools")
devtools::install_github("Asa12138/pcutils")
devtools::install_github("Asa12138/ReporterScore")
library(ReporterScore)

Need helps?

If you have any questions/issues, please visit github issue tracker.

Session information

Here is the output of sessionInfo() on the system on which this document was compiled:

sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Ventura 13.0.1
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] ReporterScore_0.1.4
#> 
#> loaded via a namespace (and not attached):
#>  [1] rstudioapi_0.14  knitr_1.45       magrittr_2.0.3   munsell_0.5.0   
#>  [5] tidyselect_1.2.0 colorspace_2.1-0 R6_2.5.1         rlang_1.1.3     
#>  [9] fastmap_1.1.0    fansi_1.0.6      dplyr_1.1.4      pcutils_0.2.5   
#> [13] tools_4.2.2      grid_4.2.2       gtable_0.3.4     xfun_0.42       
#> [17] utf8_1.2.4       cli_3.6.2        jquerylib_0.1.4  htmltools_0.5.4 
#> [21] yaml_2.3.6       digest_0.6.31    tibble_3.2.1     lifecycle_1.0.4 
#> [25] ggplot2_3.5.0    sass_0.4.4       vctrs_0.6.5      glue_1.7.0      
#> [29] cachem_1.0.6     evaluate_0.19    rmarkdown_2.25   compiler_4.2.2  
#> [33] bslib_0.4.2      pillar_1.9.0     scales_1.3.0     generics_0.1.3  
#> [37] jsonlite_1.8.4   pkgconfig_2.0.3

Reference

  1. Patil, K. R. & Nielsen, J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A 102, 2685–2689 (2005).

  2. L. Liu, R. Zhu, D. Wu, Misuse of reporter score in microbial enrichment analysis. iMeta. 2, e95 (2023).

  3. https://github.com/wangpeng407/ReporterScore

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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