Package: scMitoMut 1.3.1
Wenjie Sun
scMitoMut: Single-cell Mitochondrial Mutation Analysis Tool
This package is designed for calling lineage-informative mitochondrial mutations using single-cell sequencing data, such as scRNASeq and scATACSeq (preferably the latter due to RNA editing issues). It includes functions for mutation calling and visualization. Mutation calling is done using beta-binomial distribution.
Authors:
scMitoMut_1.3.1.tar.gz
scMitoMut_1.3.1.zip(r-4.5)scMitoMut_1.3.1.zip(r-4.4)scMitoMut_1.3.1.zip(r-4.3)
scMitoMut_1.3.1.tgz(r-4.4-x86_64)scMitoMut_1.3.1.tgz(r-4.4-arm64)scMitoMut_1.3.1.tgz(r-4.3-x86_64)scMitoMut_1.3.1.tgz(r-4.3-arm64)
scMitoMut_1.3.1.tar.gz(r-4.5-noble)scMitoMut_1.3.1.tar.gz(r-4.4-noble)
scMitoMut_1.3.1.tgz(r-4.4-emscripten)scMitoMut_1.3.1.tgz(r-4.3-emscripten)
scMitoMut.pdf |scMitoMut.html✨
scMitoMut/json (API)
NEWS
| # Install 'scMitoMut' in R: |
| install.packages('scMitoMut', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wenjie1991/scmitomut/issues
On BioConductor:scMitoMut-1.3.0(bioc 3.21)scMitoMut-1.2.0(bioc 3.20)
preprocessingsequencingsinglecellopenblascpp
Last updated 6 days agofrom:1dd76eba44. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 17 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 17 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 17 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 17 2024 |
| R-4.3-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.3-mac-x86_64 | NOTE | Dec 17 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 17 2024 |
Exports:export_afexport_binaryexport_dfexport_dtexport_pvalfilter_locget_pvalis.mtmutObjopen_h5_fileparse_mgatkparse_tableplot_af_coverageplot_heatmapprocess_locus_bmbbrm_mtmutObjrun_model_fitsubset_cellsubset_loc
Dependencies:bitbit64clicliprcolorspacecpp11crayondata.tablefansifarverggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepheatmappillarpkgconfigplyrprettyunitsprogressR6RColorBrewerRcppRcppArmadilloreadrrhdf5rhdf5filtersRhdf5librlangscalesstringistringrtibbletidyselecttzdbutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Export the mutation matrix | export_af export_binary export_df export_dt export_pval |
| Filter mutations | filter_loc |
| Print mtmutObj object | format.mtmutObj is.mtmutObj print.mtmutObj |
| Get p-value list for single locus | get_pval |
| Open H5 file | open_h5_file |
| Load mtGATK output | parse_mgatk |
| Load allele count table | parse_table |
| QC plot: 2D scatter plot for coverage ~ AF | plot_af_coverage |
| Heatmap plot | plot_heatmap |
| Fit tree models for one locus | process_locus_bmbb |
| Remove mtmutObj object | rm_mtmutObj |
| Fit binomial mixture model for every candidate locus | run_model_fit |
| scMitoMut | scMitoMut-package scMitoMut |
| Subset cell and loci | subset_cell subset_loc |
