tcR v1.1
0
Monthly downloads
Data Analysis of T-cell Receptor Repertoires
Platform for the advanced analysis of T-cell receptor repertoires data and visualisation of the analysis results.
Functions in tcR
| Name | Description | |
| get.all.substrings | Get all substrings for the given sequence. | |
| entropy | Information measures. | |
| permutedf | Shuffling data frames. | |
| AA_TABLE | Tables with genetic code. | |
| reverse.string | Reverse given character vector by the given n-plets. | |
| get.deletions.alpha | Compute the number of deletions in MiTCR data frames. | |
| rarefaction | Diversity evaluation using rarefaction. | |
| generate.tcr | Generate random nucleotide TCR sequences. | |
| check.distribution | Check for adequaty of distrubution. | |
| startmitcr | Start MiTCR directly from the package. | |
| gc.content | GC-content of a nucleotide sequences. | |
| beta.prob | List with assembling probabilities of beta chain TCRs. | |
| set.rank | Set new columns "Rank" and "Index". | |
| contamination.stats | Contamination filtering. | |
| mitcr.stats | MiTCR data frame basic statistics. | |
| inverse.simpson | Distribution evaluation. | |
| revcomp | DNA reverse complementing and translation. | |
| parse.file.list | Parse files from the given vector or list with filepaths and return list with data.frames. | |
| intersect | Intersection between sets of sequences or any elements. | |
| top.cross | Perform sequential cross starting from the top of a data.frame. | |
| parse.file | Parse input file with the given filename to a data frame. | |
| get.inframes | In-frame / out-of-frame sequences filter. | |
| barcodes.to.reads | Rearrange columns with counts for clonesets. | |
| find.clonotypes | Find target clonotypes and get columns' value corresponded to that clonotypes. | |
| set.pb | Simple functions for manipulating progress bars. | |
| vis.heatmap | Heatmap. | |
| codon.variants | Functions for working with aminoacid sequences. | |
| entropy.seg | Repertoires' analysis using information measures applied to V- and J- segment frequencies. | |
| freq.segments | V- and J-segments frequency. | |
| apply.symm | Apply function to every pair of data frames from a list. | |
| convergence.index | Compute convergence characteristics of repertoires. | |
| bootstrap.tcr | Bootstrap for data frames in package tcR. | |
| generate.kmers | Generate k-mers. | |
| cosine.similarity | Set and vector similarity measures. | |
| vis.pca | PCA result visualisation | |
| vis.top.proportions | Visualisation of top clones proportions. | |
| column.summary | Columns statistics. | |
| loglikelihood | Log-likelihood. | |
| sample2D | Get a sample from matrix with probabilities. | |
| gibbs.sampler | Gibbs Sampler. | |
| get.n.barcodes | Resample data frame using values from the column with number of clonesets. | |
| shared.repertoire | Shared TCR repertoire managing and analysis | |
| top.fun | Get samples from a repertoire slice-by-slice or top-by-top and apply function to them. | |
| spectratyping | Spectratype plot. | |
| twinsdata | Twins alpha-beta chain data | |
| segments.list | Segment data. | |
| vis.V.usage | Histogram of segments usage. | |
| pca.segments | Perform PCA on segments frequency data. | |
| assymetry | Normalised log assymetry. | |
| segments.alphabets | Alphabets of V-J segments. | |
| vis.number.count | Plot a histogram of counts. | |
| sample.clones | Get a random subset from a data.frame. | |
| tailbound.proportion | Proportions of specifyed subsets of clones. | |
| find.similar.sequences | Find similar sequences. | |
| vis.kmer.histogram | Plot of the most frequent kmers. | |
| has.class | Check if a given object has a given class. | |
| vis.count.len | Plot a histogram of lengths. | |
| vis.rarefaction | Rarefaction statistics visualisation. | |
| vis.clonal.dynamics | Visualise clonal dynamics among time points. | |
| get.kmers | Get kmers from sequences. | |
| kmer.table | Make and manage the table of the most frequent k-mers. | |
| kmer.profile | Profile of sequences of equal length. | |
| parse.folder | Parse all files to dataframes from the given path to folder. | |
| matrixdiagcopy | Copy the up-triangle matrix values to low-triangle. | |
| cosine.sharing | Shared repertoire analysis. | |
| vis.radarlike | Radar-like / spider-like plots. | |
| vis.group.boxplot | Boxplot for groups of observations. | |
| No Results! | ||
Last month downloads
Details
| Type | Package |
| Date | 2014-12-12 |
| License | Apache License 2.0 |
| LinkingTo | Rcpp |
| Packaged | 2015-01-10 18:04:26 UTC; ripley |
| NeedsCompilation | yes |
| Repository | CRAN |
| Date/Publication | 2015-01-10 19:06:05 |
| depends | base (>= 2.10) , dplyr (>= 0.4.0) , ggplot2 (>= 1.0.0) , gridExtra (>= 0.9.0) , R (>= 2.10) , reshape2 (>= 1.2.0) |
| imports | data , data.table (>= 1.9.0) , grid (>= 3.0.0) , gtable (>= 0.1.2) , Rcpp (>= 0.11.1) , roxygen2 (>= 3.0.0) , stringdist (>= 0.7.3) , utils (>= 3.1.0) |
| Contributors | Mikhail Pogorelyy, Vadim Nazarov |
Include our badge in your README
[](http://www.rdocumentation.org/packages/tcR)