Package: LEEF 0.9.1
Rainer M. Krug
LEEF: Data Package Containing Only Data and Data Information
Setup package for the LEEF pipeline which loads / installs all necessary packages and functions to run the pipeline.
Authors:
LEEF_0.9.1.tar.gz
LEEF_0.9.1.zip(r-4.5)LEEF_0.9.1.zip(r-4.4)LEEF_0.9.1.zip(r-4.3)
LEEF_0.9.1.tgz(r-4.4-any)LEEF_0.9.1.tgz(r-4.3-any)
LEEF_0.9.1.tar.gz(r-4.5-noble)LEEF_0.9.1.tar.gz(r-4.4-noble)
LEEF.pdf |LEEF.html✨
LEEF/json (API)
| # Install 'LEEF' in R: |
| install.packages('LEEF', repos = c('https://leef-uzh.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/leef-uzh/leef/issues
data-analysisdata-processingleef
Last updated 2 years agofrom:178c83e223 (on master). Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win | WARNING | Nov 05 2024 |
| R-4.5-linux | WARNING | Nov 05 2024 |
| R-4.4-win | WARNING | Nov 05 2024 |
| R-4.4-mac | WARNING | Nov 05 2024 |
| R-4.3-win | WARNING | Nov 05 2024 |
| R-4.3-mac | WARNING | Nov 05 2024 |
Exports:addadd_additoradd_archiveradd_extractoradd_pre_processorcontrol_centerinit_LEEFlist_LEEF_packagesopt_directoriesprocessprocess_raw_comp_noneregister_packagesrunrun_additorsrun_archiversrun_extractorsrun_pre_processorssplit_bemovi
Dependencies:askpassbemovi.LEEFBHBiobaseBiocGenericsbitbit64blobbootbriocachemcallrcellrangercircularclassclicpp11crayoncytolibdata.tableDBIdescdiffobjdigestdplyrdrate1071evaluatefansifastmapflowCorefsgenericsgluehmsjsonliteLEEF.archive.defaultLEEF.backend.sqliteLEEF.measurement.bemoviLEEF.measurement.flowcamLEEF.measurement.flowcytometerLEEF.measurement.manualcountLEEF.measurement.o2meterlifecycleloggitmagrittrMASSmatrixStatsmemoisemvtnormopensslpillarpkgbuildpkgconfigpkgloadplogrplyrpraiseprettyunitsprocessxprogressproxypspurrrR.methodsS3R.ooR.utilsR6randomForestRcppreadxlrematchRhdf5librlangrprojrootRProtoBufLibRSQLiteS4Vectorssettingsstringistringrsystestthattibbletidyrtidyselecttiffutf8vctrswaldowithryaml
01 Background LEEF Data
Rendered fromc_01_background_leef.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-08-26
Started: 2021-03-08
02 Pipeline Management
Rendered fromc_02_pipeline_management.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-09-09
Started: 2021-03-19
03 Manual Pipeline Management
Rendered fromc_03_running_pipeline_manual.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-03-26
Started: 2021-03-08
05 Block Storage
Rendered fromc_05_block_storage.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-05-26
Started: 2021-05-26
04 Pipeline Server Admin Guide
Rendered fromc_04_pipeline_server_admin.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-03-26
Started: 2021-03-19
1001 Start Pipeline Checklist
Rendered frome_1001_start_pipeline_checklist.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-03-26
Started: 2021-03-08
101 RRD Description
Rendered fromd_101_RRD_Description.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-08-26
Started: 2021-03-08
102 Create LEEF docker Host
Rendered fromd_102_create_LEEF_docker_host.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-08-26
Started: 2021-03-08
9999 Leef Planning
Rendered fromx_9999_Leef_Planning.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-03-26
Started: 2021-03-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add or replace a function in a queue | add add_additor add_archiver add_extractor add_pre_processor |
| Run the Control Center shiny app included in the LEEF package. | control_center |
| Create folder structure and prepares the pipeline based on the config file | init_LEEF |
| LEEF | LEEF |
| List packages on which LEEF depends from the LEEF-UZH repo | list_LEEF_packages |
| Functions to read and write options | opt_directories |
| Process all ques in the correct order | process |
| Process all queues in the correct order | process_raw_comp_none |
| Register the functions to be usedfrom packages in the config file | register_packages |
| Run process queue | run |
| Run additors queue | run_additors |
| Run archivers queue | run_archivers |
| Run extractors queue | run_extractors |
| Run pre_processors queue | run_pre_processors |
| Split bemovi filder into a number of bemovi. folders with a maximum of per_batch video files | split_bemovi |
