Man pages for alakazam
Immunoglobulin Clonal Lineage and Diversity Analysis
| ABBREV_AA | Amino acid abbreviation translations |
| AbundanceCurve-class | S4 class defining a clonal abundance curve |
| alakazam | The Alakazam package |
| alakazam-package | alakazam: Immunoglobulin Clonal Lineage and Diversity... |
| aliphatic | Calculates the aliphatic index of amino acid sequences |
| alphaDiversity | Calculate clonal alpha diversity |
| aminoAcidProperties | Calculates amino acid chemical properties for sequence data |
| baseTheme | Standard ggplot settings |
| buildPhylipLineage | Infer an Ig lineage using PHYLIP |
| bulk | Calculates the average bulkiness of amino acid sequences |
| calcCoverage | Calculate sample coverage |
| calcDiversity | Calculate the diversity index |
| ChangeoClone-class | S4 class defining a clone |
| charge | Calculates the net charge of amino acid sequences. |
| checkColumns | Check data.frame for valid columns and issue message if... |
| collapseDuplicates | Remove duplicate DNA sequences and combine annotations |
| combineIgphyml | Combine IgPhyML object parameters into a dataframe |
| countClones | Tabulates clones sizes |
| countGenes | Tabulates V(D)J allele, gene or family usage. |
| countPatterns | Count sequence patterns |
| cpuCount | Available CPU cores |
| DEFAULT_COLORS | Default colors |
| DiversityCurve-class | S4 class defining a diversity curve |
| EdgeTest-class | S4 class defining edge significance |
| estimateAbundance | Estimates the complete clonal relative abundance distribution |
| Example10x | Small example 10x Genomics Ig V(D)J sequences from CD19+ B... |
| ExampleDb | Example AIRR database |
| ExampleDbChangeo | Example Change-O database |
| ExampleTrees | Example Ig lineage trees |
| extractVRegion | Extracts FWRs and CDRs from IMGT-gapped sequences |
| getAAMatrix | Build an AA distance matrix |
| getDNAMatrix | Build a DNA distance matrix |
| getMRCA | Retrieve the first non-root node of a lineage tree |
| getPathLengths | Calculate path lengths from the tree root |
| getPositionQuality | Get a data.frame with sequencing qualities per position |
| getSegment | Get Ig segment allele, gene and family names |
| graphToPhylo | Convert a tree in igraph 'graph' format to ape 'phylo'... |
| gravy | Calculates the hydrophobicity of amino acid sequences |
| gridPlot | Plot multiple ggplot objects |
| groupGenes | Group sequences by gene assignment |
| IMGT_REGIONS | IMGT V-segment regions |
| isValidAASeq | Validate amino acid sequences |
| IUPAC_CODES | IUPAC ambiguous characters |
| junctionAlignment | Calculate junction region alignment properties |
| makeChangeoClone | Generate a ChangeoClone object for lineage construction |
| makeTempDir | Create a temporary folder |
| maskPositionsByQuality | Mask sequence positions with low quality |
| maskSeqEnds | Masks ragged leading and trailing edges of aligned DNA... |
| maskSeqGaps | Masks gap characters in DNA sequences |
| MRCATest-class | S4 class defining edge significance |
| nonsquareDist | Calculate pairwise distances between sequences |
| padSeqEnds | Pads ragged ends of aligned DNA sequences |
| pairwiseDist | Calculate pairwise distances between sequences |
| pairwiseEqual | Calculate pairwise equivalence between sequences |
| permuteLabels | Permute the node labels of a tree |
| phyloToGraph | Convert a tree in ape 'phylo' format to igraph 'graph'... |
| plotAbundanceCurve | Plot a clonal abundance distribution |
| plotDiversityCurve | Plot the results of alphaDiversity |
| plotDiversityTest | Plot the results of diversity testing |
| plotEdgeTest | Plot the results of an edge permutation test |
| plotMRCATest | Plot the results of a founder permutation test |
| plotSubtrees | Plots subtree statistics for multiple trees |
| polar | Calculates the average polarity of amino acid sequences |
| progressBar | Standard progress bar |
| rarefyDiversity | Generate a clonal diversity index curve |
| readChangeoDb | Read a Change-O tab-delimited database file |
| readFastqDb | Load sequencing quality scores from a FASTQ file |
| readIgphyml | Read in output from IgPhyML |
| seqDist | Calculate distance between two sequences |
| seqEqual | Test DNA sequences for equality. |
| SingleDb | Single sequence AIRR database |
| sortGenes | Sort V(D)J genes |
| stoufferMeta | Weighted meta-analysis of p-values via Stouffer's method |
| summarizeSubtrees | Generate subtree summary statistics for a tree |
| tableEdges | Tabulate the number of edges between annotations within a... |
| testDiversity | Pairwise test of the diversity index |
| testEdges | Tests for parent-child annotation enrichment in lineage trees |
| testMRCA | Tests for MRCA annotation enrichment in lineage trees |
| translateDNA | Translate nucleotide sequences to amino acids |
| translateStrings | Translate a vector of strings |
| writeChangeoDb | Write a Change-O tab-delimited database file |
