Man pages for ph-pham/RepSeq
Analysis of High-throughput sequencing repertoire data (RepSeqTools)
| basicIndices | updates sample data with basic statistics |
| Chaowor | Adjusted Chao1 for sampling without replacement |
| concateRepSeq | concatenate 2 RepSeqExperiment objects |
| countFeatures | count reads |
| divLevel | compute diversity indices |
| dropSamples | drop sample(s) from a RepSeqExperiment object |
| estimateSF | estimate size factor |
| filetype | get type of file |
| filterClonotypes | filter clonotypes |
| filterCount | filter clonotypes based on counts |
| filterFrequency | filter clonotypes presented in less than a proportion of... |
| getOverlaps | get shared clonotypes |
| getPrivates | get private clonotypes |
| getSingleton | get singletons |
| iChao | Improved Chao1 |
| muScore | compute multivariate score |
| muScoreM | compute pre-muScore matrix This function returns a matrix of... |
| muScoreOB | compute muScore |
| named.contr.sum | create contrast matrix from factor level names |
| normalizeCounts | Get normalized count |
| parseAdaptive | parse Adaptive tables |
| parseClonotypeR | parse ClonotypeR tables |
| parseMiXCR | parse MiXCR tables |
| parseRTCR | parse rTCR tables |
| perturbation | perturbation scores computation |
| plot2v2count | sample against sample plot |
| plotCountVJ | plot a heatmap of V-J count |
| plotDissimilarityMatrix | create heatmap of pairwise distance matrix between samples |
| plotDistribVpJ | frequency of clonotype by its rank |
| plotFrequencySpectrum | plot of frequency |
| plotFreqVpJ | plot frequency |
| plotMDS | biplot Multidimensional Scaling result |
| plotmuScore | plot heatmap of counts or percentages |
| plotPropVJ | plot V or J proportion |
| plotRenyiProfiles | plot Renyi's profiles |
| plotSpectratype | plot spectratype |
| plotSpectratypeV | plot Spectratype by V genes |
| plotVenn | plot Venn's diagram |
| rarefyRepSeqExp | down-sampling to have the same library size. |
| raretabRepSeq | compute rarefaction table for a RepSeqExperiment object |
| readClonotypes | read clonotype table |
| readClonotypeSet | read clonotype table set |
| renyiProfiles | compute Renyi's profile |
| RepSeq | RepSeq |
| RepSeqExp | build RepSeqExperiment object from clonotype tables |
| RepSeqExperiment-class | Class RepSeqExperiment |
| segmentUsage | compute usage of segments |
| toDESeq2 | RepSeqCount to DESeqDataSet |
