Provides functions for fitting discrete distribution models to count data.
  Included are the Poisson, the negative binomial, the Poisson-inverse gaussian and, most importantly,
  a new implementation of the Poisson-beta distribution (density, distribution and quantile
  functions, and random number generator) together with a needed new implementation of
  Kummer's function (also: confluent hypergeometric function of the first kind). Three
  different implementations of the Gillespie algorithm allow data simulation based on the
  basic, switching or bursting mRNA generating processes. Moreover, likelihood functions for
  four variants of each of the three aforementioned distributions are also available.
  The variants include one population and two population mixtures, both with and without
  zero-inflation. The package depends on the 'MPFR' libraries (<https://www.mpfr.org/>) which need to be installed separately 
  (see description at <https://github.com/fuchslab/scModels>).
  This package is supplement to the paper "A mechanistic model for the negative binomial distribution of single-cell mRNA counts" 
  by Lisa Amrhein, Kumar Harsha and Christiane Fuchs (2019) <doi:10.1101/657619> available on bioRxiv.

Unequal granularity of cell type annotation makes it difficult to compare scRNA-seq datasets at scale. Leveraging the ontology system for defining cell type hierarchy, 'scOntoMatch' aims to align cell type annotations to make them comparable across studies. The alignment involves two core steps: first is to trim the cell type tree within each dataset so each cell type does not have descendants, and then map cell type labels cross-studies by direct matching and mapping descendants to ancestors. Various functions for plotting cell type trees and manipulating ontology terms are also provided. In the Single Cell Expression Atlas hosted at EBI, a compendium of datasets with curated ontology labels are great inputs to this package.

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) <doi: 10.1093/bioinformatics/bty235>.
             Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>.
             Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.