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 27 days ago

softwareshinyappsvisualization

4.85 score 7 stars 2 scripts 145 downloads

appreci8R - 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 27 days ago

variantdetectiongeneticvariabilitysnpvariantannotationsequencing

3.70 score 1 scripts 184 downloads

BadRegionFinder - 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 27 days ago

coveragesequencingalignmentwholegenomeclassification

3.30 score 1 scripts 266 downloads

BBCAnalyzer - 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 27 days ago

sequencingalignmentcoveragegeneticvariabilitysnp

3.30 score 1 scripts 284 downloads