turboGliph: turboGliph: Grouping of Lymphocyte Interactions by Paratope...
In HetzDra/turboGliph: Find Specificity Groups with GLIPH and GLIPH2 Method
turboGliph R Documentation
turboGliph: Grouping of Lymphocyte Interactions by Paratope Hotspots
Description
GLIPH and GLIPH2 clusters TCRs that are predicted to bind
the same HLA-restricted peptide antigen.
Algorithm
The scripts used in this package are written based on the original scripts of GLIPH which
is in perl. The output files produced by this package are exactly similar to the
results of perl script. GLIPH in R is parallelized and optimized to run faster. For
large input, 10^5 sequences, it is about 500 times faster than the perl code. For moderate
input, 10^4 sequences, it is about 50 times faster.
Recently a new version of the package, GLIPH2, has been introduced where the main change in the
algorithm is the speed up of the analysis by substituting repeated sampling by Fisher's exact test
to assess the statistical significance of a given motif.
However in turboGliph we follow the original GLIPH but accelerate it by using appropriate R tools, efficient codes and parallelization.
Source
Glanville, Jacob, et al. "Identifying specificity groups in the T cell receptor repertoire." Nature 547.7661 (2017): 94.
Huang, Huang, et al. "Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening." Nature Biotechnology 38.10 (2020): 1194-1202.
Perl scripts from : https://github.com/immunoengineer/gliph (Aug. 2018)
HetzDra/turboGliph documentation built on Oct. 2, 2022, 2:22 a.m.
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| turboGliph | R Documentation |
turboGliph: Grouping of Lymphocyte Interactions by Paratope Hotspots
Description
GLIPH and GLIPH2 clusters TCRs that are predicted to bind the same HLA-restricted peptide antigen.
Algorithm
The scripts used in this package are written based on the original scripts of GLIPH which is in perl. The output files produced by this package are exactly similar to the results of perl script. GLIPH in R is parallelized and optimized to run faster. For large input, 10^5 sequences, it is about 500 times faster than the perl code. For moderate input, 10^4 sequences, it is about 50 times faster.
Recently a new version of the package, GLIPH2, has been introduced where the main change in the algorithm is the speed up of the analysis by substituting repeated sampling by Fisher's exact test to assess the statistical significance of a given motif. However in turboGliph we follow the original GLIPH but accelerate it by using appropriate R tools, efficient codes and parallelization.
Source
Glanville, Jacob, et al. "Identifying specificity groups in the T cell receptor repertoire." Nature 547.7661 (2017): 94.
Huang, Huang, et al. "Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening." Nature Biotechnology 38.10 (2020): 1194-1202.
Perl scripts from : https://github.com/immunoengineer/gliph (Aug. 2018)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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