Files in nriddiford/mutationProfiles
Collection of functions to explore SNV data (e.g. Mutect2/Freebayes) parsed by get_tris.pl
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/chromDist.R
R/cleanTheme.R
R/dist2motif.R
R/dist2tss.R
R/featureEnrichment.R
R/featuresHit.R
R/genTris.R
R/geneEnrichment.R
R/geneHit.R
R/genes_of_interest.R
R/getData.R
R/indels.R
R/mutSigs.R
R/mutSpectrum.R
R/rainfall.R
R/regionEnrichment.R
R/samplesPlot.R
R/setCols.R
R/sigTypes.R
R/snvStats.R
R/snvinGene.R
R/triCount.R
README.md
data/gene_lengths.txt
data/genomic_features.txt
data/tri.counts.dmel6.txt
fig_s6_e.pdf
inst/extdata/Buchon_summary_ISCs.txt
inst/extdata/annotated_indels.txt
inst/extdata/annotated_snvs.txt
inst/extdata/isc_genes_rnaSeq.txt
man/EnrichmentVolcano.Rd
man/Volcano.Rd
man/bpRegionEnrichmentPlot.Rd
man/bpSim.Rd
man/chromDist.Rd
man/cleanTheme.Rd
man/dist2motif2.Rd
man/distOverlay2.Rd
man/featureEnrichment.Rd
man/featuresHit.Rd
man/genTris.Rd
man/geneEnrichment.Rd
man/geneHit.Rd
man/generateData.Rd
man/getData.Rd
man/getTriFromFasta.Rd
man/ggVolcano.Rd
man/indel_lengths.Rd
man/mergeOverlaps.Rd
man/mutSigs.Rd
man/mutSpectrum.Rd
man/plotMonteCarlo.Rd
man/plot_indels.Rd
man/plot_snvs.Rd
man/plotdistanceOverlay2.Rd
man/rainfall.Rd
man/samplesPlot.Rd
man/setCols.Rd
man/showSamples.Rd
man/sigTypes.Rd
man/snvRegionEnrichment.Rd
man/snvSim.Rd
man/snvStats.Rd
man/snvinGene.Rd
man/subtractUnmappable.Rd
man/triFreq.Rd
man/tssDist.Rd
man/writeBed.Rd
mutationProfiles.R
mutationProfiles.Rproj
run_trinucs.sh
script/combine_muts.py
script/combinevcf.py
script/dnds_analysis.R
script/filtervcf.py
script/genomefeatures.pl
script/run_combine_vcf.sh
script/run_filtervcf.sh
script/snv2gene.pl
script/trinucs.pl
script/vcffilter.pl
