Man pages for bcRep
Advanced Analysis of B Cell Receptor Repertoire Data
| aaDistribution | Amino acid distribution of sequences |
| aaseqtab | Summary of amino acid sequences of B cells of one individual |
| aaseqtab2 | Summary of amino acid sequences of B cells of another... |
| bcRep-package | Advanced Analysis of B Cell Receptor Repertoire Data |
| clones | Grouping sequences into clones |
| clones.allind | B cell clones of 8 individuals |
| clones.CDR3Length | CDR3 length distribution of clones |
| clones.filterFunctionality | Filter for productive/unproductive clones |
| clones.filterJunctionFrame | Filter for in-frame/out-of-frame clones |
| clones.filterSize | Filter clones for their size |
| clones.giniIndex | Gini index of clones |
| clones.IDlist | Match sequence ID's and clone ID's |
| clones.ind | Data frame: clones of one individual |
| clones.shared | Shared clones between samples |
| combineIMGT | Combination of several IMGT output folders |
| compare.aaDistribution | Compare amino acid distribution of different samples |
| compare.geneUsage | Compare gene usage of different samples |
| compare.trueDiversity | Compare richness or diversity of different samples |
| dist.PCoA | Principal coordinate analysis (PCoA; multidimensional scaling... |
| geneUsage | Gene usage statistics |
| geneUsage.distance | Dissimilarity/distance indices for gene usage data |
| mutationtab | Summary of mutations cells |
| ntseqtab | Summary of nucleotide sequences of B cells of one individual |
| plotClonesCopyNumber | Copy number of clones |
| readIMGT | Read IMGT/HighV-QUEST output files |
| sequences.distance | Dissimilarity/distance indices for sequence data |
| sequences.functionality | Summary of functionality of sequences |
| sequences.geneComb | Gene/gene combinations |
| sequences.getAnyFunctionality | Filter for productive or unproductive sequences |
| sequences.getAnyJunctionFrame | Filter for in-frame or out-of-frame sequences |
| sequences.junctionFrame | Summary of junction frames of sequences |
| sequences.mutation | Basic statistics on mutations of sequences |
| sequences.mutation.AA | Detect amino acid mutations in V-, FR- or CDR-regions |
| sequences.mutation.base | Statistics about silent mutations |
| summarytab | Summary information of B cells of one individual |
| trueDiversity | True diversity of sequences |
| vgenes | VH gene usage data |
