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:
gemini_1.21.0.tar.gz
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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
- 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-1.21.0(bioc 3.21)gemini-1.20.0(bioc 3.20)
softwarecrisprbayesiandataimportcomputational-biologygenetic-interactions
Last updated 2 months agofrom:22ea9ceaf7. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:%<>%%>%gemini_boxplotgemini_calculate_lfcgemini_create_inputgemini_inferencegemini_initializegemini_plot_maegemini_prepare_inputgemini_scoreinitialize_sinitialize_tauinitialize_xinitialize_yupdate_maeupdate_s_pbupdate_tau_pbupdate_x_pbupdate_y_pb
Dependencies:askpassbase64encbslibcachemclicolorspacecpp11crosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemixtoolsmunsellnlmeopensslpbmcapplypillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalessegmentedstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml
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 |
