R Packages that start with:
A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .
Functions
- add.option()
- alternate.gene.sort()
- build.variant.specification()
- caller.overlap.venn.diagram()
- capitalize.caller()
- classify.variant()
- convert.ides.output()
- create.directories()
- date.stamp.file.name()
- extract.sample.ids()
- filter.variant.file()
- filter.variants()
- fix.lofreq.af()
- fix.names()
- fix.varscan.af()
- get.base.substitution()
- get.bed.chromosomes()
- get.buildver()
- get.colours()
- get.coverage.by.amplicon()
- get.coverage.by.sample.statistics()
- get.fasta.chromosomes()
- get.file.path()
- get.filters()
- get.gene()
- get.miniseq.sample.files()
- get.option()
- get.panel.coverage.by.gene()
- get.pool.from.panel.data()
- get.varitas.options()
- get.vcf.chromosomes()
- in.varitas.options()
- logical.to.character()
- make.command.line.call()
- mean.field.value()
- merge.ides.annotation()
- merge.variants()
- overwrite.varitas.options()
- parse.job.dependencies()
- plot.amplicon.coverage.per.sample()
- plot.coverage.by.genome.order()
- plot.coverage.by.sample()
- plot.ontarget.percent()
- plot.paired.percent()
- post.processing()
- prepare.bam.specification()
- prepare.fastq.specification()
- prepare.miniseq.specifications()
- prepare.vcf.specification()
- process.coverage.reports()
- process.sample.contamination.checks()
- process.total.coverage.statistics()
- read.all.calls()
- read.ides.file()
- read.variant.calls()
- read.yaml()
- run.alignment()
- run.alignment.sample()
- run.all.scripts()
- run.annotation()
- run.annovar.vcf()
- run.filtering.txt()
- run.ides()
- run.lofreq.sample()
- run.muse.sample()
- run.mutect.sample()
- run.post.processing()
- run.target.qc()
- run.target.qc.sample()
- run.vardict.sample()
- run.variant.calling()
- run.varitas.pipeline.hybrid()
- run.varitas.pipeline()
- run.varscan.sample()
- save.config()
- save.coverage.excel()
- save.variants.excel()
- set.varitas.options()
- split.on.column()
- sum.dp4()
- system.ls()
- tabular.mean()
- tabular.median()
- trinucleotide.barplot()
- variant.recurrence.barplot()
- variants.caller.barplot()
- variants.sample.barplot()
- verify.bam.specification()
- verify.bwa.index()
- verify.fasta.index()
- verify.fastq.specification()
- verify.sequence.dictionary()
- verify.varitas.options()
- verify.vcf.specification()
R Codes
- add.option.R
- caller.overlap.venn.diagram.R
- convert.ides.output.R
- filter.variant.file.R
- filter.variants.R
- fix.names.R
- get.coverage.by.amplicon.R
- get.coverage.by.sample.statistics.R
- get.filters.R
- get.gene.R
- get.miniseq.sample.files.R
- get.option.R
- get.varitas.options.R
- helper_functions.R
- in.varitas.options.R
- merge.variants.R
- overwrite.varitas.options.R
- plot.amplicon.coverage.per.sample.R
- plot.coverage.by.genome.order.R
- plot.coverage.by.sample.R
- plot.ontarget.percent.R
- plot.paired.percent.R
- post.processing.R
- prepare.bam.specification.R
- prepare.fastq.specification.R
- prepare.miniseq.specifications.R
- prepare.vcf.specification.R
- process.coverage.reports.R
- process.sample.contamination.checks.R
- process.total.coverage.statistics.R
- read.all.calls.R
- read.ides.file.R
- read.variant.calls.R
- run.alignment.R
- run.alignment.sample.R
- run.all.scripts.R
- run.annotation.R
- run.annovar.vcf.R
- run.filtering.txt.R
- run.ides.R
- run.lofreq.sample.R
- run.muse.sample.R
- run.mutect.sample.R
- run.post.processing.R
- run.target.qc.R
- run.target.qc.sample.R
- run.vardict.sample.R
- run.variant.calling.R
- run.varitas.pipeline.hybrid.R
- run.varitas.pipeline.R
- run.varscan.sample.R
- save.coverage.excel.R
- save.variants.excel.R
- set.varitas.options.R
- setup.R
- trinucleotide.barplot.R
- variant.recurrence.barplot.R
- variants.caller.barplot.R
- variants.sample.barplot.R
- varitas-pkg.R
- verify.bam.specification.R
- verify.bwa.index.R
- verify.fasta.index.R
- verify.fastq.specification.R
- verify.sequence.dictionary.R
- verify.varitas.options.R
- verify.vcf.specification.R
Selected R package: varitas
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