Package: ccRemover 1.0.4
Jun Li
ccRemover: Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data
Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. Submitted. Different from previous methods, ccRemover implements a mechanism that formally tests whether a component is cell-cycle related or not, and thus while it often thoroughly removes the cell-cycle effect, it preserves other features/signals of interest in the data.
Authors:
ccRemover_1.0.4.tar.gz
ccRemover_1.0.4.tar.gz(r-4.5-noble)ccRemover_1.0.4.tar.gz(r-4.4-noble)
ccRemover_1.0.4.tgz(r-4.4-emscripten)ccRemover_1.0.4.tgz(r-4.3-emscripten)
ccRemover.pdf |ccRemover.html✨
ccRemover/json (API)
| # Install 'ccRemover' in R: |
| install.packages('ccRemover', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- dat - A simulated scRNA-Seq data.
- human_cell_cycle_genes - Homo Sapien genes which are annotated to the cell-cycle
- mouse_cell_cycle_genes - Mus Musculus genes which are annotated to the cell-cycle
- t.cell_data - Single-Cell RNA-Seq data from differentiating T-helper cells
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 7 years agofrom:39249bf6eb. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 17 2024 |
| R-4.5-linux | OK | Dec 17 2024 |
Exports:bootstrap_diffccRemovergene_indexerget_diffhello
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculates the difference in the loading score for cell-cycle and control genes | bootstrap_diff |
| Removes the effect of the cell-cycle | ccRemover |
| A simulated scRNA-Seq data. | dat |
| Identifies genes annotated to the cell-cycle | gene_indexer |
| Calculates the average load difference between the cell-cycle genes and control genes for each component. | get_diff |
| Hello, World! | hello |
| Homo Sapien genes which are annotated to the cell-cycle | human_cell_cycle_genes |
| Mus Musculus genes which are annotated to the cell-cycle | mouse_cell_cycle_genes |
| Single-Cell RNA-Seq data from differentiating T-helper cells | t.cell_data |