Package: scimo 0.0.2

Antoine BICHAT

scimo: Extra Recipes Steps for Dealing with Omics Data

Omics data (e.g. transcriptomics, proteomics, metagenomics...) offer a detailed and multi-dimensional perspective on the molecular components and interactions within complex biological (eco)systems. Analyzing these data requires adapted procedures, which are implemented as steps according to the 'recipes' package.

Authors:Antoine BICHAT [aut, cre], Julie AUBERT [ctb]

scimo_0.0.2.tar.gz
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scimo.pdf |scimo.html✨
scimo/json (API)
NEWS

# Install 'scimo' in R:

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

Bug tracker:https://github.com/abichat/scimo/issues

Datasets:

cheese_abundance - Abundance of Fungal Communities in Cheese
cheese_taxonomy - Abundance of Fungal Communities in Cheese
pedcan_expression - Gene Expression of Pediatric Cancer

On CRAN:

5.08 score 3 stars 4 scripts 423 downloads 9 exports 54 dependencies

Last updated 6 months agofrom:00934c97ca. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:%>%step_aggregate_hclust step_aggregate_list step_rownormalize_tss step_select_background step_select_cv step_select_kruskal step_select_wilcoxon step_taxonomy

Dependencies:class cli clock codetools cpp11 data.table diagram digest dplyr fansi future future.apply generics globals glue gower hardhat ipred KernSmooth lattice lava lifecycle listenv lubridate magrittr MASS Matrix nnet numDeriv parallelly pillar pkgconfig prodlim progressr purrr R6 Rcpp recipes rlang rpart shape SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs withr

Pediatric cancers

Rendered frompedcan.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-07
Started: 2024-02-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Abundance of Fungal Communities in Cheese	cheese_abundance cheese_taxonomy
Gene Expression of Pediatric Cancer	pedcan_expression
Feature aggregation step based on a hierarchical clustering	step_aggregate_hclust tidy.step_aggregate_hclust
Feature aggregation step based on a defined list	step_aggregate_list tidy.step_aggregate_list
Feature normalization step using total sum scaling	step_rownormalize_tss tidy.step_rownormalize_tss
Feature selection step using background level	step_select_background tidy.step_select_background
Feature selection step using the coefficient of variation	step_select_cv tidy.step_select_cv
Feature selection step using Kruskal test	step_select_kruskal tidy.step_select_kruskal
Feature selection step using Wilcoxon test	step_select_wilcoxon tidy.step_select_wilcoxon
Taxonomic clades feature generator	step_taxonomy tidy.step_taxonomy