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immunarch  

Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
View on CRAN: Click here


Download and install immunarch package within the R console
Install from CRAN:
install.packages("immunarch")

Install from Github:
library("remotes")
install_github("cran/immunarch")

Install by package version:
library("remotes")
install_version("immunarch", "0.9.1")



Attach the package and use:
library("immunarch")
Maintained by
Vadim I. Nazarov
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-05-13
Latest Update: 2022-12-15
Description:
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) .
How to cite:
Vadim I. Nazarov (2020). immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires. R package version 0.9.1, https://cran.r-project.org/web/packages/immunarch. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.6.4 (2020-05-13 10:00), 0.6.5 (2020-06-14 19:40), 0.6.6 (2021-07-07 10:20), 0.6.7 (2021-10-29 14:00), 0.6.8 (2022-05-04 17:30), 0.6.9 (2022-05-30 21:00), 0.7.0 (2022-08-10 00:00), 0.8.0 (2022-10-18 00:22), 0.9.0 (2022-12-15 16:00)
Other packages that cited immunarch R package
View immunarch citation profile
Other R packages that immunarch depends, imports, suggests or enhances
Complete documentation for immunarch
Functions, R codes and Examples using the immunarch R package
Some associated functions: aa_properties . aa_table . add_class . apply_symm . bcrdata . bunch_translate . check_distribution . coding . dbAnnotate . dbLoad . dot-quant_column_choice . entropy . fixVis . geneUsage . geneUsageAnalysis . gene_segments . gene_stats . getKmers . group_from_metadata . has_class . immdata . immunr_data_format . immunr_hclust . immunr_pca . inc_overlap . matrixdiagcopy . pubRep . pubRepApply . pubRepFilter . pubRepStatistics . public_matrix . repAlignLineage . repClonalFamily . repClonality . repDiversity . repExplore . repFilter . repGermline . repLoad . repOverlap . repOverlapAnalysis . repSample . repSave . repSomaticHypermutation . scdata . select_barcodes . select_clusters . seqCluster . seqDist . set_pb . spectratype . split_to_kmers . switch_type . top . trackClonotypes . vis.clonal_family . vis.clonal_family_tree . vis.immunr_chao1 . vis.immunr_clonal_prop . vis.immunr_dynamics . vis.immunr_exp_vol . vis.immunr_gene_usage . vis.immunr_hclust . vis.immunr_inc_overlap . vis.immunr_kmeans . vis.immunr_kmer_table . vis.immunr_mds . vis.immunr_ov_matrix . vis.immunr_public_repertoire . vis.immunr_public_statistics . vis . vis.step_failure_ignored . vis_bar . vis_box . vis_circos . vis_heatmap . vis_heatmap2 . vis_hist . vis_immunr_kmer_profile_main . vis_public_clonotypes . vis_public_frequencies . vis_textlogo . 
Some associated R codes: RcppExports.R . align_lineage.R . annotation.R . clonality.R . clustering.R . data_docs.R . dimensions.R . distance.R . diversity.R . dynamics.R . explore.R . filters.R . gene_usage.R . gene_usage_analysis.R . germline.R . immunarch-package.R . immunr_data_format.R . info_theory.R . io-parsers.R . io-savers.R . io-utility.R . io.R . kmers.R . overlap.R . overlap_analysis.R . phylip.R . preprocessing.R . public.R . sampling.R . seqCluster.R . shiny.R . singlecell.R . somatic_hypermutation.R . spectratyping.R . tools.R . vis.R .  Full immunarch package functions and examples
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