clevRvis - Visualization Techniques for Clonal Evolution
clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.
Last updated 5 months ago
softwareshinyappsvisualization
4 stars 4.60 score 113 dependenciesappreci8R - appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.
Last updated 5 months ago
variantdetectiongeneticvariabilitysnpvariantannotationsequencing
3.70 score 156 dependenciesBBCAnalyzer - BBCAnalyzer: an R/Bioconductor package for visualizing base counts
BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.
Last updated 5 months ago
sequencingalignmentcoveragegeneticvariabilitysnp
3.30 score 70 dependenciesBadRegionFinder - BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.
Last updated 5 months ago
coveragesequencingalignmentwholegenomeclassification
2.30 score 94 dependencies