Package: gemini 1.21.0

Sidharth Jain

gemini: GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

GEMINI uses log-fold changes to model sample-dependent and independent effects, and uses a variational Bayes approach to infer these effects. The inferred effects are used to score and identify genetic interactions, such as lethality and recovery. More details can be found in Zamanighomi et al. 2019 (in press).

Authors:Mahdi Zamanighomi [aut], Sidharth Jain [aut, cre]

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gemini.pdf |gemini.html✨
gemini/json (API)
NEWS

# Install 'gemini' in R:

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

Bug tracker:https://github.com/sellerslab/gemini/issues

Datasets:

Input - Input object from Big Papi
Model - Model object from Big Papi
counts - Big Papi counts matrix
guide.annotation - Big Papi guide annotations
sample.replicate.annotation - Big Papi sample and replicate annotations

On BioConductor:gemini-1.19.0(bioc 3.20)gemini-1.18.0(bioc 3.19)

software crispr bayesian dataimport computational-biology genetic-interactions

6.02 score 15 stars 9 scripts 132 downloads 7 mentions 19 exports 75 dependencies

Last updated 23 days agofrom:22ea9ceaf7. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 30 2024

Exports:%<>%%>%gemini_boxplot gemini_calculate_lfc gemini_create_input gemini_inference gemini_initialize gemini_plot_mae gemini_prepare_input gemini_score initialize_s initialize_tau initialize_x initialize_y update_mae update_s_pb update_tau_pb update_x_pb update_y_pb

Dependencies:askpass base64enc bslib cachem 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 kernlab knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime mixtools munsell nlme openssl pbmcapply pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown sass scales segmented stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

A guide to the GEMINI R package

Mahdi Zamanighomi and Sidharth Jain

Rendered fromgemini-quickstart.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-06-24
Started: 2019-03-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Median normalization	.median_normalize
Compound pipe	%<>%
Pipe	%>%
Big Papi counts matrix	counts
gemini_boxplot	gemini_boxplot
Calculate log-fold change	gemini_calculate_lfc
gemini_create_input	gemini_create_input
gemini_inference	gemini_inference
gemini_initialize	gemini_initialize
Parallelization in GEMINI	gemini_parallelization
MAE plot	gemini_plot_mae
Prepare input before Model creation	gemini_prepare_input
Scoring Combination Effect	gemini_score
Big Papi guide annotations	guide.annotation
initialize_s	initialize_s
initialize_tau	initialize_tau
intialize_x	initialize_x
initialize_y	initialize_y
Input object from Big Papi	Input
Model object from Big Papi	Model
Big Papi sample and replicate annotations	sample.replicate.annotation
Gene hashing	Sgene2Pguides_hash
Guide hashing	Sguide2Pguides_hash
update_mae	update_mae
update_s	update_s_pb
update_tau_pb	update_tau_pb
update_x_p	update_x_pb
update_y_pb	update_y_pb