Package: directPA 1.5.1

directPA: Direction Analysis for Pathways and Kinases

Direction analysis is a set of tools designed to identify combinatorial effects of multiple treatments/conditions on pathways and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics data. See Yang P et al (2014) <doi:10.1093/bioinformatics/btt616>; and Yang P et al. (2016) <doi:10.1002/pmic.201600068>.

Authors:Pengyi Yang & Ellis Patrick

directPA_1.5.1.tar.gz
directPA_1.5.1.zip(r-4.5)directPA_1.5.1.zip(r-4.4)directPA_1.5.1.zip(r-4.3)
directPA_1.5.1.tgz(r-4.4-any)directPA_1.5.1.tgz(r-4.3-any)
directPA_1.5.1.tar.gz(r-4.5-noble)directPA_1.5.1.tar.gz(r-4.4-noble)
directPA_1.5.1.tgz(r-4.4-emscripten)directPA_1.5.1.tgz(r-4.3-emscripten)
directPA.pdf |directPA.html✨
directPA/json (API)

# Install 'directPA' in R:

install.packages('directPA', repos = c('https://pyanglab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pyanglab/directpa/issues

Datasets:

HEK - Phosphoproteomics of HEK-293E
PM - Plasma Membrame Protoemics Data
Pathways.KEGG - KEGG pathway annotations
Pathways.reactome - Reactome pathway annotations
PhosphoELM.human - PhosphoELM annotations for human
PhosphoELM.mouse - PhosphoELM annotations for mouse
PhosphoSite.human - PhosphoSitePlus annotations for human
PhosphoSite.mouse - PhosphoSitePlus annotations for mouse

On CRAN:

9 exports 1.27 score 71 dependencies 1 dependents 31 scripts 355 downloads

Last updated 10 months agofrom:6aa81fc102. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 09 2024
R-4.5-win	OK	Sep 09 2024
R-4.5-linux	OK	Sep 09 2024
R-4.4-win	OK	Sep 09 2024
R-4.4-mac	OK	Sep 09 2024
R-4.3-win	OK	Sep 09 2024
R-4.3-mac	OK	Sep 09 2024

Exports:directExplorer2d directPA geneStats kinasePA pathwayStats perturbPlot2d perturbPlot3d rotate2d rotate3d

Dependencies:askpass base64enc bslib cachem calibrate cli colorspace cpp11 crosstalk curl data.table digest dplyr evaluate fansi farver fastmap fontawesome fs generics ggplot2 glue gtable highr htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown sass scales stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Direction Pathway Analysis Package	directPA-package
Batch Direction Analysis in 2-dimentional space	directExplorer2d
Direction Analysis for Pathways	directPA
Molecule Level Statistics	geneStats
Phosphoproteomics of HEK-293E	HEK
Direction Analysis for Kinases	kinasePA
KEGG pathway annotations	Pathways.KEGG
Reactome pathway annotations	Pathways.reactome
Pathway Level Statistics	pathwayStats
Perturbation Plot	perturbPlot2d
Perturbation Plot 3D	perturbPlot3d
PhosphoELM annotations for human	PhosphoELM.human
PhosphoELM annotations for mouse	PhosphoELM.mouse
PhosphoSitePlus annotations for human	PhosphoSite.human
PhosphoSitePlus annotations for mouse	PhosphoSite.mouse
Plasma Membrame Protoemics Data	PM
Polar Coordinates Rotation	rotate2d
Spherical Coordinates Rotation	rotate3d