R-universe search: immunogenomics

Showing 6 of total 6 results (show query)

immunogenomics

harmony:Fast, Sensitive, and Accurate Integration of Single Cell Data

Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi:10.1038/s41592-019-0619-0>. Package includes a standalone Harmony function and interfaces to external frameworks.

Maintained by Ilya Korsunsky. Last updated 4 months ago.

algorithm data-integration scrna-seq openblas cpp

20.0 match 554 stars 13.74 score 5.5k scripts 8 dependents

bioc

IgGeneUsage:Differential gene usage in immune repertoires

Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.

Maintained by Simo Kitanovski. Last updated 5 months ago.

differentialexpression regression genetics bayesian biomedicalinformatics immunooncology mathematicalbiology b-cell-receptor bcr-repertoire differential-analysis differential-gene-expression high-throughput-sequencing immune-repertoire immune-repertoire-analysis immune-repertoires immunogenomics immunoglobulin immunoinformatics immunological-bioinformatics immunology tcr-repertoire vdj-recombination cpp

10.0 match 6 stars 5.92 score 1 scripts

sjmack

HLAtools:Toolkit for HLA Immunogenomics

A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.

Maintained by Steven Mack. Last updated 12 days ago.

3.3 match 4 stars 6.21 score 7 scripts 1 dependents

bioc

midasHLA:R package for immunogenomics data handling and association analysis

MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.

Maintained by Maciej Migdał. Last updated 5 months ago.

cellbiology genetics statisticalmethod

2.9 match 4.30 score 3 scripts

bioc

SingleCellAlleleExperiment:S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes

Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.

Maintained by Jonas Schuck. Last updated 2 months ago.

datarepresentation infrastructure singlecell transcriptomics geneexpression genetics immunooncology dataimport

0.5 match 7 stars 6.30 score 12 scripts

cran

Platypus:Single-Cell Immune Repertoire and Gene Expression Analysis

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Maintained by Alexander Yermanos. Last updated 5 months ago.

0.5 match 4.58 score 38 scripts