alakazam
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Alakazam
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Installing Released Versions
Building Development Versions
Package Overview
Description
File I/O
Sequence cleaning
Lineage reconstruction
Lineage topology analysis
Diversity analysis
Ig and TCR sequence annotation
Sequence distance calculation
Amino acid propertes
References
Release Notes
Version 1.3.0: September 29, 2023
Version 1.2.1: September 19, 2022
Version 1.2.0: October 31, 2021
Version 1.1.0: February 6, 2021
Version 1.0.2: July 17, 2020
Version 1.0.1: May 8, 2020
Version 0.3.0: July 17, 2019
Version 0.2.11: September 12, 2018
Version 0.2.10: March 30, 2018
Version 0.2.9: March 21, 2018
Version 0.2.8: September 21, 2017
Version 0.2.7: June 12, 2017
Version 0.2.6: March 21, 2017
Version 0.2.5: August 5, 2016
Version 0.2.4: July 20, 2016
Version 0.2.3: February 22, 2016
Version 0.2.2: January 29, 2016
Version 0.2.1: December 18, 2015
Version 0.2.0: June 15, 2015
Version 0.2.0.beta-2015-05-30: May 30, 2015
Version 0.2.0.beta-2015-05-26: May 26, 2015
Version 0.2.0.beta-2015-05-05: May 05, 2015
Related Projects
Vignettes
How to read and write files
Reading data
Writing data
Basic gene usage analysis
Example data
Tabulate V(D)J allele, gene or family usage by sample
Tabulating gene abundance using additional groupings
Amino acid physicochemical property analysis
Example data
Calculate the properties of amino acid sequences
Default scales
Analysis of clonal abundance and diversity
Example data
Generate a clonal abundance curve
Generate a diversity curve
View diversity tests at a fixed diversity order
Reconstruction of Ig lineage trees
Example data
Preprocess a clone
Run PHYLIP
Plotting of the lineage tree
Batch processing lineage trees
Converting between graph, phylo, and newick formats
Topology analysis of lineage trees
Example data
Plotting annotations on a tree
Summarizing node properties
Counting and testing node annotation relationships
Counting and testing MRCA annotations
Using sequencing quality scores
Example data
Load quality scores
Mask low quality positions
Help Topics
File I/O
readChangeoDb
writeChangeoDb
readIgphyml
combineIgphyml
readFastqDb
Sequence Cleaning and Manipulation
collapseDuplicates
maskSeqEnds
maskSeqGaps
padSeqEnds
translateDNA
isValidAASeq
getPositionQuality
maskPositionsByQuality
junctionAlignment
Lineage Reconstruction
buildPhylipLineage
graphToPhylo
phyloToGraph
makeChangeoClone
ChangeoClone class
Lineage Topology Analysis
getMRCA
getPathLengths
permuteLabels
summarizeSubtrees
tableEdges
testEdges
testMRCA
plotEdgeTest
plotMRCATest
plotSubtrees
EdgeTest class
MRCATest class
Diversity Analysis
calcCoverage
calcDiversity
countClones
estimateAbundance
alphaDiversity
plotAbundanceCurve
plotDiversityCurve
plotDiversityTest
AbundanceCurve class
DiversityCurve class
Ig and TCR Sequence Annotation
countGenes
sortGenes
groupGenes
getSegment
extractVRegion
Sequence Distance Calculation
getAAMatrix
getDNAMatrix
seqDist
seqEqual
pairwiseDist
pairwiseEqual
nonsquareDist
Amino Acid Propertes
aminoAcidProperties
countPatterns
Aliphatic
Bulk
Charge
Gravy
Polar
Miscellaneous
baseTheme
checkColumns
cpuCount
gridPlot
makeTempDir
progressBar
stoufferMeta
translateStrings
Data and Constants
ExampleDb
ExampleDbChangeo
Example10x
ExampleTrees
SingleDb
ABBREV AA
IUPAC CODES
DEFAULT COLORS
IMGT REGIONS
Deprecated
rarefyDiversity
testDiversity
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