ClonoCalc and ClonoPlot: Immune repertoire analysis from raw files to publication figures with graphical user interface

BMC Bioinformatics

Volumn 18, Issue 1, 2017, Pages

  Fähnrich, Anke ^a   Krebbel, Moritz ^b   Decker, Normann ^b   Leucker, Martin ^b   Lange, Felix D ^b   Kalies, Kathrin ^a   Möller, Steffen ^c  

^a Institute of Anatomy   (Germany)

^b Institute for Software Engineering and Programming Languages   (Germany)

^c Institute for Biostatistics and Informatics in Medicine and Ageing Research   (Germany)

Author keywords

Graphical user interface; Immune repertoire analysis; Next generation sequencing

Indexed keywords

ANIMALS; CELL MEMBRANES; DATA HANDLING; GRAPHICAL USER INTERFACES; OPEN SOURCE SOFTWARE; PIPELINE PROCESSING SYSTEMS;

B CELL RECEPTOR; GRAPHICAL USER INTERFACES (GUI); IMMUNE FUNCTION; IMMUNE REPERTOIRE ANALYSIS; NEXT-GENERATION SEQUENCING; OPEN SOURCE DEVELOPMENT; PAIRED-END READS; SCIENTIFIC DISCIPLINE;

USER INTERFACES;

LYMPHOCYTE ANTIGEN RECEPTOR;

ALGORITHM; ANIMAL; BIOLOGY; COMPUTER INTERFACE; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOLOGY; INTERNET; METABOLISM;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; RECEPTORS, ANTIGEN, B-CELL; RECEPTORS, ANTIGEN, T-CELL; SEQUENCE ANALYSIS, DNA; USER-COMPUTER INTERFACE;

EID: 85014936523     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-017-1575-2     Document Type: Article

References (9)

1. Nikolich-Zugich J, Slifka MK, Messaoudi I. The many important facets of T-cell repertoire diversity. Nat Rev Immun. 2004; 4:123-32.
2. Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - The rise of next-generation repertoire analysis. Front Immunol. 2014; 3:413.
3. Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, Chudakov DM. MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods. 2015; 12:380-1.
4. Yu Y, Ceredig R, Seoighe C. LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins. Nucleic Acids Res. 2016; 4:4.
5. Nazarov VI, Pogorelyy MV, Komech EA, Zvyagin IV, Bolotin DA, Shugay M, Chudakov DM, Mamedov IZ. tcR: an R package for T cell receptor repertoire advanced data analysis. BMC Bioinforma. 2015; 16:175-80.
6. Zhang H, Meltzer P, Davis S. RCircos: an R package for Circos 2D track plots. BMC Bioinforma. 2013; 14:244.
7. Gordon A. FASTX Barcode Splitter. http://hannonlab.cshl.edu/fastx_toolkit/.
8. Urbanek S. Rserve - A Fast Way to Provide R Functionality to Applications. In: Proc. of the 3rd International Workshop on Distributed Statistical Computing. DSC: 2003. p. 1609-395. ISSN 1609-395X.
9. Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLOS Comput Biol. 2015; 11:e1004503.