by John D. Gagnon University of California, San Francisco
Overview Installation Usage Session info License
A shinyapp-based GUI to visualize miR-15/16 differential expression data along with AGO2 HITS-CLIP data for each gene.
install.packages(“remotes”)
remotes::install_github("jgagnon/DE.AHC”)
library(DE.AHC)
runDEAHCapp()
| Gene | logFC | PValue | FDR | WT_1 | WT_2 | WT_3 | cKO_1 | cKO_2 | cKO_3 | | :--- | :---- | :------- | :-------- | :---- | :---- | :---- | :----- | :----- | :----- | | Cd28 | 2.4 | 3.42e-05 | 0.0004244 | 50 | 48 | 49 | 62 | 58 | 60 | | etc… | etc… | etc… | etc… | etc… | etc… | etc… | etc… | etc… | etc… |
| Gene | Location | miR | Targetscan | Sum | | :--- | :------- | :------------ | :--------- | :--- | | Cd28 | 3UTR | mmu-miR-16-5p | TRUE | 2899 | | etc… | etc… | etc… | etc… | etc… |
Here is the output of sessionInfo()
on the system on which this
package was developed:
sessionInfo()
#> R version 3.5.1 (2018-07-02)
#> Platform: x86_64-apple-darwin17.6.0 (64-bit)
#> Running under: macOS High Sierra 10.13.6
#>
#> Matrix products: default
#> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
#>
#> locale:
#> [1] en_US.UTF-8/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
#>
#> loaded via a namespace (and not attached):
#> [1] compiler_3.5.1 backports_1.1.2 magrittr_1.5 rprojroot_1.3-2
#> [5] tools_3.5.1 htmltools_0.3.6 yaml_2.2.0 Rcpp_0.12.18
#> [9] stringi_1.2.4 rmarkdown_1.10 highr_0.7 knitr_1.20
#> [13] stringr_1.3.1 digest_0.6.17 evaluate_0.11
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