Package: effectR 1.0.3

effectR: Predicts Oomycete Effectors

Predicts cytoplasmic effector proteins using genomic data by searching for motifs of interest using regular expression searches and hidden Markov models (HMM) based in Haas et al. (2009) <doi:10.1038/nature08358>.

Authors:Javier Tabima [aut, cre], Niklaus J. Grunwald [ths]

effectR_1.0.3.tar.gz
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effectR_1.0.3.tgz(r-4.4-any)effectR_1.0.3.tgz(r-4.3-any)
effectR_1.0.3.tar.gz(r-4.5-noble)effectR_1.0.3.tar.gz(r-4.4-noble)
effectR_1.0.3.tgz(r-4.4-emscripten)effectR_1.0.3.tgz(r-4.3-emscripten)
effectR.pdf |effectR.html✨
effectR/json (API)
NEWS

# Install 'effectR' in R:

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

Bug tracker:https://github.com/tabima/effectr/issues

Datasets:

candidate.rxlr - An example of 'effector.summary' output

On CRAN:

5 exports 1 stars 1.59 score 70 dependencies 3 mentions 13 scripts 188 downloads

Last updated 6 years agofrom:8c2bd005ff. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 01 2024
R-4.5-win	NOTE	Sep 01 2024
R-4.5-linux	NOTE	Sep 01 2024
R-4.4-win	NOTE	Sep 01 2024
R-4.4-mac	NOTE	Sep 01 2024
R-4.3-win	NOTE	Sep 01 2024
R-4.3-mac	NOTE	Sep 01 2024

Exports:effector.summary hmm.logo hmm.search regex.search shiny.effectR

Dependencies:ade4 base64enc bslib cachem cli colorspace commonmark crayon digest evaluate fansi farver fastmap fontawesome fs ggplot2 glue gridExtra gtable highr htmltools httpuv isoband jquerylib jsonlite knitr labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme pillar pixmap pkgconfig plyr promises R6 rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rlang rmarkdown sass scales segmented seqinr shiny sourcetools sp stringi stringr tibble tinytex utf8 vctrs viridis viridisLite withr xfun xtable yaml

effectR: An R package to call oomycete effectors

Javier F. Tabima

Rendered fromeffectR.Rmdusingknitr::rmarkdownon Sep 01 2024.

Last update: 2018-09-29
Started: 2017-06-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
An example of `effector.summary` output	candidate.rxlr
Returns non-redundant sequences from hmm.search or regex.search and generates a motif table	effector.summary
effectR: An R Package to Call Oomycete Effectors	effectR-package effectR
Plots the relative frequencies of each position for 'hmmsearch' table.	hmm.logo
Searching for motifs using HMM searches	hmm.search
Searching for motifs using regular expressions (REGEX)	regex.search
Function to run the effectR package using a shiny app	shiny.effectR