R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
All

Data Type

Packages
Functions
Images
Data set

Classification

Results 1 - 10 of 82 found.
[1] < 1 2 3 4 5 6 7 8 9 > [9] Sort:

geneUsage (Package: tcR) : Gene usage.

Compute frequencies or counts of gene segments ("V / J - usage").

● Data Source: CranContrib
● Keywords:
● Alias: geneUsage
● 0 images

entropy.seg (Package: tcR) : Repertoires' analysis using information measures applied to V- and J- segment frequencies.

Information approach to repertoire analysis. Function entropy.seg applies Shannon entropy to V-usage and hence measures variability of V-usage. Function js.div.seg applied Jensen-Shannon divergence to V-usage of two or more data frames and hence measures distance among this V-usages.

● Data Source: CranContrib
● Keywords:
● Alias: entropy.seg, js.div.seg
● 0 images

vis.gene.usage (Package: tcR) : Histogram of segments usage.

Plot a histogram or a grid of histograms of V- / J-usage.

● Data Source: CranContrib
● Keywords:
● Alias: vis.J.usage, vis.V.usage, vis.gene.usage
● 0 images

mutated.neighbours (Package: tcR) : Get vertex neighbours.

Get all properties of neighbour vertices in a mutation network of specific vertices.

● Data Source: CranContrib
● Keywords:
● Alias: mutated.neighbours
● 0 images

parse.folder (Package: tcR) : Parse input table files with immune receptor repertoire data.

Load the TCR data from the file with the given filename to a data frame or load all files from the given folder to a list of data frames. The folder must contain onky files with the specified format. Input files could be either text files or archived with gzip ("filename.txt.gz") or bzip2 ("filename.txt.bz2"). For a general parser see parse.cloneset.

● Data Source: CranContrib
● Keywords:
● Alias: parse.file, parse.file.list, parse.folder, parse.immunoseq, parse.immunoseq2, parse.immunoseq3, parse.imseq, parse.migec, parse.migmap, parse.mitcr, parse.mitcrbc, parse.mixcr, parse.tcr, parse.vdjtools
● 0 images

top.cross (Package: tcR) : Perform sequential cross starting from the top of a data frame.

top.cross - get top crosses of the given type between each pair of the given data.frames with top.cross function.

● Data Source: CranContrib
● Keywords:
● Alias: top.cross, top.cross.plot, top.cross.vec
● 0 images

get.all.substrings (Package: tcR) : Get all substrings for the given sequence.

Get all substrings for the given sequence.

● Data Source: CranContrib
● Keywords:
● Alias: get.all.substrings
● 0 images

set.rank (Package: tcR) : Set new columns "Rank" and "Index".

Set new columns "Rank" and "Index":

● Data Source: CranContrib
● Keywords:
● Alias: set.index, set.rank
● 0 images

entropy (Package: tcR) : Information measures.

Functions for information measures of and between distributions of values.

● Data Source: CranContrib
● Keywords:
● Alias: entropy, js.div, kl.div
● 0 images

cosine.sharing (Package: tcR) : Shared repertoire analysis.

Functions for computing statistics and analysis of shared repertoire of sequences.

● Data Source: CranContrib
● Keywords:
● Alias: cosine.sharing, shared.clones.count, shared.representation, shared.summary
● 0 images