Man pages for HatsuneCode/TrustVDJ
Tools for Immune Repertoire Analysis
| addClonotype | Combine Clonotype Object |
| addConsensus | Combine Consensus Object |
| appendFile | Append Large Files |
| build_Ensembl_reference | Build Ensembl database reference |
| build_IgBlast_reference | Build NCBI-Igblast database reference |
| build_IMGT_reference | Build IMGT database reference |
| build_viruSite_reference | Build viruSite database reference |
| cbinds | Combine Two Data Frame by Columns |
| checkDup | Check Duplicated Value |
| checkIn | Check a Name in Names |
| checkName | Check Name in an VDJ Object |
| checkSub | Check Subset Value |
| Circos | Plot Circos |
| cloneAbundance | Estimate clonotype abundance |
| cloneShanno | Estimate Clonotype Shannon |
| CloneSize | Estimate Clonotype clone size |
| CloneSizeFisher | Fisher Test for Clone Size |
| clonotype-class | The Clonotype Class |
| ClonotypeFromDataframe | Create Clonotype Object from Data Frame |
| consensus-class | The Consensus Class |
| ConsensusFromDataframe | Create Consensus Object from Data Frame |
| corTest | Test for Correlation |
| CreateVdjObject | Create a VDJ Object from a VDJ sample object list |
| CreateVdjSample | Create a VDJ Sample Object from Data Frame |
| df_chain | Make a Single Chain Information |
| distribute | distribution of round numeric |
| dot-Read10x_clonotype | Read 10x Clonotype File |
| dot-Read10x_consensus | Read 10x Consensus File |
| dot-Read10x_contig | Read 10x Contig File |
| dot-ReadAIRR | Read AIRR File. |
| dot-ReadTrust_BarcodeReport | Read TRUST4 Barcode_report File. |
| dot-ReadTrust_Report | Read TRUST4 Report File. |
| Download | Download files retryable |
| fetchCdr3 | Fetch CDR3dna or CDR3aa in a Consensus Class |
| fetchVDJ | Fetch VDJ Genes in a Consensus Class |
| fetchVJab | Fetch VJ-AB in a Consensus Class |
| fetchVJpair | Fetch VJ Pair in a Consensus Class |
| filterFasta | Filter fasta file by target chromosomes |
| filterGtf | Filter gtf file by target chromosomes |
| findCDR3Motif | Find CDR3 Motif in K-mer and Position |
| findListName | Find List Name |
| findMotif | Find Characters Motif in K-mer |
| Fisher | Fisher's Exact Test |
| getCDS | Get CDS Sequence from a Fasta file by GTF file |
| GroupCDR3byMotif | Group CDR3 by motif |
| have | Check Values |
| htmlHref | Get HTML href content |
| htmlText | Get HTML text content |
| Ifnone | Default for NULL and NA Value |
| Ifnull | Default for NULL Value |
| Logo | Plot character logo |
| makePair | Make Pair Names |
| makePct | Show Number as Percentage |
| MergeClonotype | Merge Clonotype of VDJ Sample Objects |
| MergeConsensus | Merge Consensus of VDJ Sample Objects |
| MergeVdjSamples | Merge VDJ Sample Objects |
| min_max | Dispersion Normalization |
| NameVdjSample | Name an object of VDJ sample |
| none | Check NA Values in a Data Frame |
| objSize | Report the Space Allocated for an Object in Mb |
| pick | Pick Field |
| Pie | Plot Pie |
| rbinds | Combine Two Data-frame by Rows |
| Read10x | Read AIRR/10x Report Files |
| ReadTrust | Read AIRR/TRUST4 Report Files |
| RenameVdjSample | Reame an object of VDJ sample |
| Sankey | Plot VJab Sankey |
| sepInteger | Separate Positive Integer |
| show-clonotype-method | Overview of the Clonotype Class |
| show-consensus-method | Overview of the Consensus Class |
| show-Trust-method | Overview of the Trust Class |
| show-VDJ-method | Overview of the VDJ Class |
| show-VDJsample-method | Overview of the VDJsample Class |
| subsetCloneSize | Subset clonotype by clone size |
| subsetClonotype | Subset Clonotype Object |
| subsetConsensus | Subset Consensus Object |
| TableCDR3 | Table CDR3dna or CDR3aa in Each Name |
| TableVDJ | Table VDJ Genes in Each Name |
| TableVJab | Table VJ-AB in Each Name |
| TableVJpair | Table VJ Pairs in Each Name |
| timer | Time Record |
| topClone | Show Top Clonotypes |
| Trust-class | The Trust Class |
| UniqueClonotype | Unique Clonotype Object |
| Upset | Plot UpSet |
| VDJ-class | The VDJ class |
| VDJsample-class | The VDJ Sample Class |
