Showing 4 of total 4 results (show query)
cbiit
LDlinkR:Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest
Provides access to the 'LDlink' API (<https://ldlink.nih.gov/?tab=apiaccess>) using the R console. This programmatic access facilitates researchers who are interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393> data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying germline variants in human population groups of interest. For more details, please see Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Maintained by Timothy A. Myers. Last updated 11 months ago.
ld-calculatorldlinkldlink-apildlink-webtoollinkage-disequilibriumpopulation-genetics
28.3 match 58 stars 9.21 score 206 scripts 1 dependents
myles-lewis
locuszoomr:Gene Locus Plot with Gene Annotations
Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Maintained by Myles Lewis. Last updated 13 days ago.
3.8 match 40 stars 7.43 score 50 scripts
bioc
ldblock:data structures for linkage disequilibrium measures in populations
Define data structures for linkage disequilibrium measures in populations.
Maintained by VJ Carey. Last updated 5 months ago.
1.8 match 3.30 score 10 scripts
cran
haploR:Query 'HaploReg', 'RegulomeDB'
A set of utilities for querying 'HaploReg' <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php>, 'RegulomeDB' <https://www.regulomedb.org/regulome-search/> web-based tools. The package connects to 'HaploReg', 'RegulomeDB' searches and downloads results, without opening web pages, directly from R environment. Results are stored in a data frame that can be directly used in various kinds of downstream analyses.
Maintained by Ilya Y. Zhbannikov. Last updated 1 years ago.
1.5 match 1 stars 3.24 score