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.

Title: An L1-Version of the Spectral Clustering
Authors@R: c(person("Camille", "Champion", role = "aut"),
person("Magali", "Champion", role = c("aut","cre"),email="magali.champion@u-paris.fr" ))
Description: Provides an l1-version of the spectral clustering algorithm devoted to robustly clustering highly perturbed graphs using l1-penalty. This algorithm is described with more details in the preprint C. Champion, M. Champion, M. Blazère, R. Burcelin and J.M. Loubes, "l1-spectral clustering algorithm: a robust spectral clustering using Lasso regularization" (2021).
Imports: Rcpp (>= 0.12.5), stats, graphics, igraph, Matrix, NMI,
Packaged: 2021-03-04 10:49:50 UTC; mchampion

Packaged: 2021-03-12 06:49:01 UTC; mchampion

Imports: Rcpp (>= 0.12.5), stats, dplyr, graphics, igraph, Matrix,
aricode, grDevices, glmnet, ggplot2, cvTools
Packaged: 2021-10-20 05:52:19 UTC; mchampion

aricode, grDevices, caret, glmnet, ggplot2, cvTools
Packaged: 2022-01-04 15:03:25 UTC; mchampion

Description: Provides an l1-version of the spectral clustering algorithm devoted to robustly clustering highly perturbed graphs using l1-penalty. This algorithm is described with more details in the preprint C. Champion, M. Champion, M. Blazère, R. Burcelin and J.M. Loubes, "l1-spectral clustering algorithm: a spectral clustering method using l1-regularization" (2022).
Packaged: 2022-01-26 16:29:51 UTC; mchampion