1. kleinstein
  2. B Cell Repertoires
  3. alakazam

Source

alakazam /

Filename Size Date modified Message
R
data
data-raw
docs
inst
src
tests
vignettes
99 B
1. Moved ExampleDb from a file in `extdata` to a data object and added documentation for the ExampleDb.
735 B
Added tag Version 0.2.7 - Rcpp Fix for changeset 96f9e7e4e561
1.7 KB
Fix for case where phylip's output has only one block. Fix for case where
4.0 KB
Swapped progress bars to use the progress package.
7.1 KB
1. Bumped version and date.
1.2 KB
Fixed changeo link in README.
228 B
Switched to single R+python test image.
3.0 KB
Added gene usage vignette to toc.

Alakazam

Alakazam is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides a set of tools to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties, with a focus on high-throughput immunoglobulin (Ig) sequencing.

Alakazam serves five main purposes:

  1. Providing core functionality for other R packages in the Immcantation framework. This includes common tasks such as file I/O, basic DNA sequence manipulation, and interacting with V(D)J segment and gene annotations.
  2. Providing an R interface for interacting with the output of the pRESTO and Change-O tool suites.
  3. Performing lineage reconstruction on clonal populations of Ig sequences and analyzing the topology of the resultant lineage trees.
  4. Performing clonal abundance and diversity analysis on lymphocyte repertoires.
  5. Performing physicochemical property analyses of lymphocyte receptor sequences.