Package: scMitoMut 1.1.0
Wenjie Sun
scMitoMut: Single-cell Mitochondrial Mutation Analysis Tool
This package is designed for analyzing 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 filtering and visualization. In the future, the visualization tool will become an independent package. Mutation filtering is performed by fitting a statistical model to account for various sources of noise, including PCR error, sequencing error, mtDNA sampling and/or heteroplasmy dynamics. The model tests whether the observed allele frequency of a locus in a cell can be explained by the noise model. If not, we classify it as a mutation. The input for this analysis is the allele frequency. The noise model consists of three independent models: binomial, binomial-mixture, and beta-binomial models.
Authors:
scMitoMut_1.1.0.tar.gz
scMitoMut_1.1.0.zip(r-4.5)scMitoMut_1.1.0.zip(r-4.4)scMitoMut_1.1.0.zip(r-4.3)
scMitoMut_1.1.0.tgz(r-4.4-x86_64)scMitoMut_1.1.0.tgz(r-4.3-x86_64)
scMitoMut_1.1.0.tar.gz(r-4.5-noble)scMitoMut_1.1.0.tar.gz(r-4.4-noble)
scMitoMut_1.1.0.tgz(r-4.4-emscripten)scMitoMut_1.1.0.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-1.1.0(bioc 3.20)scMitoMut-1.0.0(bioc 3.19)
Last updated 2 months agofrom:954512abb7
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.tablefansifarverggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepheatmappillarpkgconfigplyrprettyunitsprogressR6RColorBrewerRcppRcppArmadilloreadrrhdf5rhdf5filtersRhdf5librlangscalesstringistringrtibbletidyselecttzdbutf8vctrsviridisLitevroomwithrzlibbioc
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 |
| Subset cell and loci | subset_cell subset_loc |
