In langmead-lab/snapcount: R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
library(snapcount)

snapcount

Overview

snapcount is a package for interfacing with Snaptron's REST API.

Installation

# Install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("langmead-lab/snapcount")

Usage

snapcount can be used with either a procedural interface

library(snapcount)

query_jx(compilation = "gtex", regions = "CD99")
query_jx(compilation = "gtex", regions = "CD99", range_filters = samples_count == 10)

Or using the query-builder class

sb <- SnaptronQueryBuilder$new()
sb$compilation("gtex")$regions("CD99")$query_jx()

# sb$from_url("http://snaptron.cs.jhu.edu/gtex/bases?regions=BRCA1&sids=50099,50102,50113")$query_gene()

Reference

For more information on Snaptron please visit: http://snaptron.cs.jhu.edu/index.html.

langmead-lab/snapcount documentation built on May 1, 2022, 4:27 a.m.