Files in trichelab/MTseeker
Bioconductor Tools for Human Mitochondrial Variant Analysis
.gitignore
DESCRIPTION
Makefile
NAMESPACE
R/MAlignments.R
R/MAlignmentsList.R
R/MTHGVS.R
R/MTcircos.R
R/MTcomplex.R
R/MTcoverage.R
R/MVRanges.R
R/MVRangesList.R
R/anno_rCRS.R
R/byStrand.R
R/chrominfo.rCRS.R
R/decomposeAndCalcConsequences.R
R/depthFilterAndHaploMask.R
R/exportFilteredAsVcf.R
R/filterMT.R
R/filterMTvars.R
R/fixMetadata.R
R/fpFilter_RSRS.R
R/fpFilter_Triska.R
R/genMTcircos.R
R/getMT.R
R/getProteinImpact.R
R/getScReads.R
R/haploMask.R
R/haplomask_whitelist.R
R/hg19TorCRS.R
R/importVCF.R
R/injectMTvariants.R
R/lift_up_to_rCRS.R
R/locateMTvariants.R
R/mtAnno.R
R/mtGenes.R
R/mtGenes.rCRS.R
R/newFilterMT.R
R/pileupMT.R
R/pileupXenograft.R
R/rCRSeq.R
R/rawMTreads.R
R/s4Methods.R
R/scanMT.R
R/validMetadata.R
README.md
data/MTmouseAnno.rds
data/NC_005089seq.rda
data/anno_rCRS.rda
data/chrominfo.rCRS.rda
data/fpFilter_RSRS.rda
data/fpFilter_Triska.rda
data/haplomask_whitelist.rda
data/hg19TorCRS.rda
data/mtAnno.rCRS.rda
data/mtDf.rds
data/mtGenes.rCRS.rda
data/mtGenes.rda
data/mtMouseGFF.rds
data/mtMouse_gr.rds
data/rCRSeq.rda
inst/extdata/MTmouseCircos.R
inst/extdata/NC_005089.fa
inst/extdata/RO_1.png
inst/extdata/RO_NKS_filtered.png
inst/extdata/RSRS.fa
inst/extdata/RSRS.fa.fai
inst/extdata/biohazard.svg
inst/extdata/hg19.chrM.fa
inst/extdata/hg19.chrM.fa.fai
inst/extdata/mitocarta2.R
inst/extdata/mm10.chrM.fa
inst/extdata/mm10.chrM.fa.fai
inst/extdata/mtAnno.R
inst/extdata/mtAnno.rCRS.bed
inst/extdata/mtCN.png
inst/extdata/mtColors.csv
inst/extdata/mtComplexes.svg
inst/extdata/rCRS.R
inst/extdata/rCRS.fa
inst/extdata/rCRS.fa.fai
inst/extdata/rCRS.gff3
inst/extdata/rCRS_original.fa
man/MAlignments-class.Rd
man/MAlignments-methods.Rd
man/MAlignmentsList-class.Rd
man/MAlignmentsList-methods.Rd
man/MTHGVS.Rd
man/MTcircos.Rd
man/MTcomplex.Rd
man/MTcoverage.Rd
man/MVRanges-class.Rd
man/MVRanges-methods.Rd
man/MVRangesList-class.Rd
man/MVRangesList-methods.Rd
man/anno_rCRS.Rd
man/byStrand.Rd
man/chrominfo.rCRS.Rd
man/decomposeAndCalcConsequences.Rd
man/depthFilterAndHaploMask.Rd
man/exportFilteredAsVcf.Rd
man/filterMT.Rd
man/filterMTvars.Rd
man/fixMetadata.Rd
man/fpFilter_RSRS.Rd
man/fpFilter_Triska.Rd
man/getMT.Rd
man/getProteinImpact.Rd
man/getScReads.Rd
man/haploMask.Rd
man/haplomask_whitelist.Rd
man/hg19TorCRS.Rd
man/importVCF.Rd
man/injectMTVariants.Rd
man/lift_up_to_rCRS.Rd
man/locateMTvariants.Rd
man/mtAnno.Rd
man/mtGenes.Rd
man/mtGenes.rCRS.Rd
man/newFilterMT.Rd
man/pileupMT.Rd
man/pileupXenograft.Rd
man/rCRSeq.Rd
man/rawMTreads.Rd
man/s4Methods.Rd
man/scanMT.Rd
man/validMetadata.Rd
man/vcf2mvrl.Rd
vignettes/RO_NKS_filtered.png
vignettes/oncocytomas.Rmd
