Title: Changing the Reference Group without Re-Running the Model
Author: Ziqiang Lin, Eugene M Laska, Carole E Siegel, Wangjian Zhang, Qiaoxuan Lin, Bo Ye.
Description: To re-calculate the coefficients and the standard deviation when changing the reference group.

Title: Covariance Based Decomposition of Bulk Expression with
Authors@R: c(person("Ali", "Karimnezhad", role = c("aut", "cre", "ctb"),
Description: Provides accurate cell type proportion estimation by incorporating covariance structure in both single-cell and bulk RNA-seq datasets into the analysis. For a related work, see Jew, B. et al. (2020) <dio:10.1038/s41467-020-15816-6>.
Imports: nlshrink, limSolve, Biobase, BisqueRNA, methods, plyr, Seurat,

Title: Covariance Based Single-Cell Decomposition of Bulk Expression
Description: Provides accurate cell type proportion estimation by incorporating covariance structure in both single-cell and bulk RNA-seq datasets into the analysis. For more detail, see Karimnezhad, A. (2022) <doi:10.1101/2022.05.13.491858>.

Title: Fitting and Tuning Regularized Cause-Specific Cox Models with
Authors@R: c(person(given = "Shahin",family = "Roshani",role = c("aut", "cre", "cph"),email = "s.roshani@nki.nl",comment = c(ORCID = "0000-0001-7518-157X")))
Description: Flexible tools to fit, tune and obtain absolute risk predictions from regularized cause-specific cox models with elastic-net penalty.

Title: CRISPR-Based Salmonella Enterica Serotype Analyzer
person("Xia", "Zhang", role = c("aut", "cre"), email = "zhangxia9403@gmail.com"),
person("Lang", "Yang", role = "aut", email = "ylang1992@126.com"))
Description: Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Serotype identification is the most commonly used typing method to characterize Salmonella isolates. However, experimental serotyping needs great cost on manpower and resources. Recently, we found that the newly incorporated spacer in the clustered regularly interspaced short palindromic repeat (CRISPR) could serve as an effective marker for typing of Salmonella. It was further revealed by Li et. al (2014) <doi:10.1128/JCM.00696-14> that recognized types based on the combination of two newly incorporated spacer in both CRISPR loci showed high accordance with serotypes. Here, we developed an R package 'CSESA' to predict the serotype based on this finding. Considering it’s time saving and of high accuracy, we recommend to predict the serotypes of unknown Salmonella isolates using 'CSESA' before doing the traditional serotyping.