LINCSanalytics

LINCSanalytics is a computational platform built on top of the open source Cloudera Hadoop distribution.

More information can be found here: https://figshare.com/articles/LINCSAnalytics_An_integrated_platform_for_the_efficient_query_and_computation_across_diverse_LINCS_signatures/4962719

An R package, called LINCSanalytics, enables computational biologists, and in general R users, to fully access the platform.

To install the package from R use the install_github function from package devtools:

install.packages("devtools")
library(devtools)
install_github("schurerlab/LINCSanalytics")
library(LINCSanalytics)

Current version includes the following functions:

available_data(), lists the available LINCS datasets, their ID and assay name

get_L1000ph1_expression(), retrieves L1000 data from LINCS Phase 1, weighted average of replicates z-scores (level 5)

get_L1000ph2_expression(), retrieves L1000 data from LINCS Phase 2, weighted average of replicates z-scores (level 5)

get_p100_expression(), retrieves P100 data, plate normalized log2 fold change.

get_gcp_expression(), retrieves Global Chromatin Profiling (GCP) data, plate normalized log2 fold change

get_kinomescan(), retrieves KINOMEscan assay data, percent control or Kd.

get_kinatv(), retrieve KiNativ assay data, percent inhibition or IC50

predict_kinase(), predicts kinase inhibition probability for a given small molecule smiles (Knet model)

Help is available using:

?function_name