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¶ Author: Brian M. Schilder ¶

¶ README updated: Dec-22-2022 ¶

echotabix: Converts genomic data files to tabix format

(including liftover, sorting, compression, and indexing steps) with a single function. Retrieves local or remote tabix VCF/tabular files with helper functions for creating queries from subsets of genomic data (e.g GWAS/QTL loci, genomic ranges). Multiple methods available at each step, including wrapper functions for an up-to-date, conda-based installation of htslib tools.

This R package is part of the echoverse suite that supports echolocatoR: an automated genomic fine-mapping pipeline.

If you use echotabix, please cite:

Brian M Schilder, Jack Humphrey, Towfique Raj (2021) echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline, Bioinformatics; btab658, https://doi.org/10.1093/bioinformatics/btab658

Installation

if(!require("remotes")) install.packages("remotes")

remotes::install_github("RajLabMSSM/echotabix")
library(echotabix)

Documentation

Website

Getting started

Contact

Brian M. Schilder, Bioinformatician II
Raj Lab
Department of Neuroscience, Icahn School of Medicine at Mount Sinai