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LymAnalyzer specifications

Information


Unique identifier OMICS_10193
Name LymAnalyzer
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Cathal Seoighe

Publication for LymAnalyzer

LymAnalyzer citations

 (3)
library_books

Overview of methodologies for T cell receptor repertoire analysis

2017
BMC Biotechnol
PMCID: 5504616
PMID: 28693542
DOI: 10.1186/s12896-017-0379-9

[…] data containing UMIs are MIGEC [] and pRESTO []. The tools listed above are mainly used for primary analysis, as the recovery of TCR sequences from raw data and successive clustering and annotation. LymAnalyzer additionally contains a feature for SNP calling and sequence mutation trees generation for IGs.Further (secondary) data analysis of the immune repertoire classically involves the calculati […]

library_books

3D: diversity, dynamics, differential testing – a proposed pipeline for analysis of next generation sequencing T cell repertoire data

2017
BMC Bioinformatics
PMCID: 5327583
PMID: 28241742
DOI: 10.1186/s12859-017-1544-9

[…] iversity and dynamics of the repertoire. For example, miXCR [] is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. The more comprehensive software, LymAnalyzer [], consists of four functional components: VDJ gene alignment, CDR3 extraction, polymorphism analysis and lineage mutation tree construction. sciReptor [] is a flexible toolkit for the pr […]

library_books

High Throughput Sequencing Based Immune Repertoire Study during Infectious Disease

2016
Front Immunol
PMCID: 5005336
PMID: 27630639
DOI: 10.3389/fimmu.2016.00336

[…] ew V–D–J gene annotation tools based on various algorithms are reported, such as IgBLAST (), iHMMune-align (), and Decombinator (, ) (Table ). In addition, many integrated bioinformatic tools (MiTCR, LymAnalyzer, Change-O, etc.) for data processing are developed recently (–) (Table ), which provides various statistical approaches for diversity estimation, repertoire comparison, clustering analysis […]

Citations

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LymAnalyzer institution(s)
School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, University Road, Galway, Ireland
LymAnalyzer funding source(s)
European Union Seventh Framework Programme (FP7/2007–2013) under grant agreement 317040 (QuanTI)

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