immcantation.r-universe.dev

[immcantation] dowser 2.4.2.999

kenneth.b.hoehn@dartmouth.edu (Kenneth Hoehn) — Thu, 18 Jun 2026 18:33:08 GMT

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) , Hoehn et al (2021) .

[immcantation] shazam 1.3.2.999

susanna.marquez@yale.edu (Susanna Marquez) — Tue, 26 May 2026 08:50:38 GMT

Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) , Yaari, et al (2012) , Yaari, et al (2013) , Cui, et al (2016) .

[immcantation] scoper 1.5.0.999

susanna.marquez@yale.edu (Susanna Marquez) — Mon, 25 May 2026 17:15:59 GMT

Provides a computational framework for identification of B cell clones from Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main functions are included (identicalClones, hierarchicalClones, and spectralClones) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) . Nouri N and Kleinstein SH (2019) . Gupta NT, et al. (2017) .

[immcantation] alakazam 1.4.3.999

susanna.marquez@yale.edu (Susanna Marquez) — Fri, 01 May 2026 07:53:08 GMT

Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) , Stern, Yaari and Vander Heiden, et al (2014) .

[immcantation] tigger 1.1.3

susanna.marquez@yale.edu (Susanna Marquez) — Mon, 13 Apr 2026 19:01:21 GMT

Infers the V genotype of an individual from immunoglobulin (Ig) repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences. Citations: Gadala-Maria, et al (2015) , Gadala-Maria, et al (2019) .