Showing 5 of total 5 results (show query)
immunomind
immunarch:Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Maintained by Vadim I. Nazarov. Last updated 1 years ago.
airr-analysisb-cell-receptorbcrbcr-repertoirebioinformaticsigig-repertoireimmune-repertoireimmune-repertoire-analysisimmune-repertoire-dataimmunoglobulinimmunoinformaticsimmunologyrep-seqrepertoire-analysissingle-cellsingle-cell-analysist-cell-receptortcrtcr-repertoirecpp
316 stars 9.49 score 203 scripts
djhshih
argparser:Command-Line Argument Parser
Cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script.
Maintained by David J. H. Shih. Last updated 1 years ago.
6.02 score 1.6k scripts 1 dependents
jmbarbone
fuj:Functions and Utilities for Jordan
Provides core functions and utilities for packages and other code developed by Jordan Mark Barbone.
Maintained by Jordan Mark Barbone. Last updated 25 days ago.
2 stars 4.48 score 8 scripts 1 dependents
t-kalinowski
envir:Manage R Environments Better
Provides a small set of functions for managing R environments, with defaults designed to encourage usage patterns that scale well to larger code bases. It provides: import_from(), a flexible way to assign bindings that defaults to the current environment; include(), a vectorized alternative to base::source() that also default to the current environment; and attach_eval() and attach_source(), a way to evaluate expressions in attached environments. Together, these (and other) functions pair to provide a robust alternative to base::library() and base::source().
Maintained by Tomasz Kalinowski. Last updated 12 months ago.
15 stars 4.20 score 21 scripts
ben-schwen
holiglm:Holistic Generalized Linear Models
Holistic generalized linear models (HGLMs) extend generalized linear models (GLMs) by enabling the possibility to add further constraints to the model. The 'holiglm' package simplifies estimating HGLMs using convex optimization. Additional information about the package can be found in the reference manual, the 'README' and the accompanying paper <doi:10.18637/jss.v108.i07>.
Maintained by Benjamin Schwendinger. Last updated 3 months ago.
3 stars 2.78 score