Reconstruction of Clones from Integration Site Readouts and Visualization
Create a stacked area plot that represents the abundance of integratio...
Calculate the bw index
Converts a matrix to relative abundances
Evaluate a clustering using the given method
Evaluate a clustering using the bw index
Evaluate a clustering using a custom evaluation function
Evaluate a clustering using the dunn index
Evaluate a clustering using the point-biserial index
Evaluate a clustering using the SD-index
Evaluate a clustering using the silhouette index
Filters a matrix of readouts for the n biggest IS at a certain measure...
Filters a matrix of readouts for IS that have a minimum occurrence in ...
Combines columns that have the same name. The columns are joined addit...
Shortens the rownames of a readout matrix to the shortest distinct pre...
Filters for columns containing a certain substring.
Splits a vector of strings by a given regexp, selects and rearranges t...
Filters a vector of names and returns the shortest common prefix.
Filters for a minimum number of time points/measurements
Removes columns that only contain 0 or NA.
Removes rows that only contain 0 or NA.
Finds the best number of clusters according to silhouette
Generate a similarity matrix
Get the default ggplot color palette or a color palette based on the g...
Show line plots of all integration sites over time, split into facets ...
Normalizes a time course using a given mapping from integration sites ...
Plots the clustering based on a clustering object
Plots the similarity of integration sites
Plots time series data, which consists of multiple measurements over t...
Plots R^2 of two integration sites
Apply a clustering algorithm to a given time course.
Calculate the k-medoids clustering for a given time course.
Apply a clustering algorithm recursively to a given time course.
Plot the relationship of integration sites as a graph.
Tools necessary to reconstruct clonal affiliations from temporally and/or spatially separated measurements of viral integration sites. For this means it utilizes correlations present in the relative readouts of the integration sites. Furthermore, facilities for filtering of the data and visualization of different steps in the pipeline are provided with the package.