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l1kdeconv  

Deconvolution for LINCS L1000 Data
View on CRAN: Click here


Download and install l1kdeconv package within the R console
Install from CRAN:
install.packages("l1kdeconv")

Install from Github:
library("remotes")
install_github("cran/l1kdeconv")

Install by package version:
library("remotes")
install_version("l1kdeconv", "1.2.0")



Attach the package and use:
library("l1kdeconv")
Maintained by
Zhao Li
[Scholar Profile | Author Map]
First Published: 2017-04-18
Latest Update: 2017-07-08
Description:
LINCS L1000 is a high-throughput technology that allows the gene expression measurement in a large number of assays. However, to fit the measurements of ~1000 genes in the ~500 color channels of LINCS L1000, every two landmark genes are designed to share a single channel. Thus, a deconvolution step is required to infer the expression values of each gene. Any errors in this step can be propagated adversely to the downstream analyses. We present a LINCS L1000 data peak calling R package l1kdeconv based on a new outlier detection method and an aggregate Gaussian mixture model. Upon the remove of outliers and the borrowing information among similar samples, l1kdeconv shows more stable and better performance than methods commonly used in LINCS L1000 data deconvolution.
How to cite:
Zhao Li (2017). l1kdeconv: Deconvolution for LINCS L1000 Data. R package version 1.2.0, https://cran.r-project.org/web/packages/l1kdeconv. Accessed 07 Apr. 2025.
Previous versions and publish date:
1.1.0 (2017-04-18 01:00)
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Complete documentation for l1kdeconv
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