Package: mitoClone2 1.11.0

Benjamin Story

mitoClone2: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.

Authors:Benjamin Story [aut, cre], Lars Velten [aut], Gregor Mönke [aut]

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mitoClone2.pdf |mitoClone2.html✨
mitoClone2/json (API)
NEWS

# Install 'mitoClone2' in R:

install.packages('mitoClone2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/benstory/mitoclone2/issues

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library
c++– GNU Standard C++ Library v3

Datasets:

M_P1 - Mitochondrial exclusionlist
M_P2 - Mitochondrial exclusionlist
N_P1 - Mitochondrial exclusionlist
N_P2 - Mitochondrial exclusionlist

On BioConductor:mitoClone2-1.11.0(bioc 3.20)mitoClone2-1.10.0(bioc 3.19)

bioconductor-package

19 exports 0.49 score 97 dependencies

Last updated 2 months agofrom:191fc47739

Exports:bam2R_10x baseCountsFromBamList clusterMetaclones getAlleleCount getCloneLikelihood getMut2Clone getVarsCandidate mitoPlot mut2GR mutationCallsFromCohort mutationCallsFromExclusionlist mutationCallsFromMatrix overwriteMetaclones plotClones pullcountsVars quick_cluster removeWindow setVarsCandidate varCluster

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools colorspace cpp11 crayon curl DBI deepSNV DelayedArray fansi farver fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pheatmap pillar pkgconfig plogr plyr png R6 RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble UCSC.utils utf8 VariantAnnotation vctrs VGAM viridisLite withr XML XVector yaml zlibbioc

Computation of phylogenetic trees and clustering of mutations

Lars Velten

Rendered fromclustering.Rmdusingknitr::rmarkdownon Jun 26 2024.

Last update: 2021-07-15
Started: 2021-06-20

Variant Calling

Benjamin Story

Rendered fromoverview.Rmdusingknitr::rmarkdownon Jun 26 2024.

Last update: 2021-07-19
Started: 2021-06-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Read nucleotide counts from a 10x Genomics .bam file	bam2R_10x
Create a list object from a list of single-cell BAM files where each contains a matrix of the of AGCT nt counts at chosen sites	baseCountsFromBamList
Cluster mutations into clones - following the tree structure	clusterMetaclones
Mitochondrial exclusionlist	data exclusionlists M_P1 M_P2 N_P1 N_P2
mutationCalls counts accessor	getAlleleCount
mutationCalls accessors	getCloneLikelihood getConfidence getMainClone getMut2Clone
mutationCalls cluster accessor	getVarsCandidate
Plot clone-specific variants in circular plots	mitoPlot
Convert mutation string to GRanges	mut2GR
mutationCalls class	mutationCalls mutationCalls-class
Create a mutationCalls objects from nucleotide base calls and defines a exclusionlist (cohort)	mutationCallsFromCohort
Create a mutationCalls object from nucleotide base calls using a exclusionlist (single individual)	mutationCallsFromExclusionlist
mutationCalls constructor	mutationCallsFromMatrix
Manually overwrite clustering of mutations into clones	overwriteMetaclones
Plot clonal assignment of single cells	plotClones
Pull variant counts	pullcountsVars
Quick clustering of mutations	quick_cluster
Remove mutations that occuring at the same site	removeWindow
mutationCalls cluster setter	setVarsCandidate
Inference of mutational trees by of single cell mutational status	varCluster