Integrative Clustering of Multiple Genomic Dataset
Prabhakar Chalise, Rama Raghavan, Brooke Fridley
Carries out integrative clustering analysis using multiple types of genomic dataset.
R (>= 2.14), MASS, NMF, mclust, cluster, InterSIM

Carries out integrative clustering analysis using multiple types of genomic dataset using integrative Non-negative Matrix factorization.
R (>= 3.5), MASS, NMF, mclust, cluster, InterSIM

c(person("Chixiang","Chen",email="chencxxy@hotmail.com",role=c("cre","aut")),
person("Yuk Yee","Leung",email="yyee@mail.med.upenn.edu",role="aut"),
person("Matei","Lonita",email="matei.ionita@pennmedicine.upenn.edu",role="aut"),
person("Li-San","Wang",email="lswang@pennmedicine.upenn.edu",role="aut"),
person("Mingyao","Li",email="mingyao@pennmedicine.upenn.edu",role="aut"))
We developed the Integrated and Robust Deconvolution algorithm to infer cell-type proportions from target bulk RNA-seq data. This package is able to effectively integrate deconvolution results from multiple scRNA-seq datasets and calibrates estimates from reference-based deconvolution by taking into account extra biological information as priors. Moreover, the proposed algorithm is robust to inaccurate external information imposed in the deconvolution system.
Rcpp (>= 0.11.0), L1pack, limSolve, cowplot, ggplot2,
pheatmap, stats,DescTools, mgcv, reshape2, Biobase
Chixiang Chen [cre, aut],
Yuk Yee Leung [aut],
Matei Lonita [aut],
Li-San Wang [aut],
Mingyao Li [aut]

Rcpp (>= 0.11.0), limSolve, cowplot, ggplot2, pheatmap,
stats,DescTools, mgcv, reshape2

person("Yue", "Bai", email = "bai42@wisc.edu", role = c("aut", "cre"))

Joint Modelling of the Gene-Expression and Bioassay Data, Taking
Care of the Effect Due to a Fingerprint Feature
Offers modelling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.

Joint Modeling of the Gene-Expression and Bioassay Data, Taking
Care of the Effect Due to a Fingerprint Feature
Offers modeling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.