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The 'Rariant' package offers the framework to identify and characterize shifts of variant frequencies in a comparative setting from high-throughput short-read sequencing data. It estimates shifts in the non-consensus variant frequency and provides confidence estimates that allow for a quantitative assessment of presence or absence of variants. The vignette accompanying the package gives a detailed explanation and outlines a typical workflow on real data.
● Data Source:
BioConductor
● Keywords: package
● Alias: Rariant, Rariant-package
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Multiple testing adjustment of confidence levels, as proposed by Benjamini and Yekutieli.
● Data Source:
BioConductor
● Keywords:
● Alias: ciAdjustLevel
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ciAssessment
(Package: Rariant) :
Assessment of CI methods
Functions to compute the coverage probability of a confidence interval method.
● Data Source:
BioConductor
● Keywords:
● Alias: coverageProbability
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Utility functions to find confidence intervals that (a) overlap a certain value ('ciOutside', 'ciCovers') and (b) different confidence intervals overlap ('ciOverlap').
● Data Source:
BioConductor
● Keywords:
● Alias: ciCovers, ciOutside, ciOverlap, ciWidth
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Color and fill scales used for plotting in Rariant.
● Data Source:
BioConductor
● Keywords:
● Alias: baseFillScale, eventFillScale, rateFillScale, verdictColorScale
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Utility functions to convert between 'GRanges' and 'character' objects.
● Data Source:
BioConductor
● Keywords:
● Alias: gr2pos, pos2gr
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Heatmap with the evidence of variant evidences.
● Data Source:
BioConductor
● Keywords:
● Alias: evidenceHeatmap
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tallyPlot
(Package: Rariant) :
Mismatch plot from BAM files
Create a mismatch plot from a list of BAM files directly.
● Data Source:
BioConductor
● Keywords:
● Alias: tallyPlot
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mismatchUtils
(Package: Rariant) :
Tally processing low-level functions
Functions for processing position-specific base count tables (tallies) and extracting mismatches counts.
● Data Source:
BioConductor
● Keywords:
● Alias: callConsensus, mismatchCount, mismatchUtils, selectStrand, seqDepth
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multiCalls
(Package: Rariant) :
Multi call processing
Utilities for processing matched calls from multipe samples.
● Data Source:
BioConductor
● Keywords:
● Alias: filterCalls, findCalls, mergeCalls, updateCalls
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