Title: Pathway analysis methods for genomewide association data
Description: The two Bayesian hierarchical pathway analysis methods Sparse normal/Adaptive lasso and Normal/Bayes factors proposed by Evangelou et al (2013) are implemented. Further, the well-known Fisher's method is implemented

Title: Pathway Analysis Methods for Genomewide Association Data
Description: Bayesian hierarchical methods for pathway analysis of genomewide association data: Normal/Bayes factors and Sparse Normal/Adaptive lasso. The Frequentist Fisher's product method is included as well.
Packaged: 2015-12-08 12:35:35 UTC; marinaevangelou

Title: Identify Intra and Inter-Donor Variations in Bulk or Single Cell
Description: It is a platform for analyzing longitudinal data from bulk as well as single cell datasets. It allows to identify variations in molecular features within and across donors over longitudinal time points. The analysis can be done on bulk expression dataset without known cell type information or single cell with cell type/user-defined groups. It allows to infer stable and variable features in given donor and each cell type (or user defined group). The outlier analysis can be performed to identify technical/biological perturbed samples in donor/participant. Further, differential analysis can be performed to decipher time-wise changes in gene expression in a cell type.
Depends: R (>= 4.0), methods, grid, graphics, stats, grDevices
Imports: Seurat (>= 3.9), ggrepel (>= 0.9), pbapply (>= 1.4), lme4 (>=
Rtsne (>= 0.15), knitr(>= 1.30), dplyr, ggplot2, reshape2,
ComplexHeatmap, circlize, cowplot, pheatmap, tidyverse, utils
Packaged: 2022-05-11 16:21:00 UTC; suhas.vasaikar

Packaged: 2022-05-31 23:38:18 UTC; suhas.vasaikar

Packaged: 2022-08-17 22:03:26 UTC; suhas.vasaikar

Title: Rank Aggregation with Partition Mallows Model
Description: Rank aggregation aims to achieve a better ranking list given multiple observations. 'PAMA' implements Partition-Mallows model for rank aggregation. Both Bayesian inference and Maximum likelihood estimation (MLE) are provided. It can handle partial list as well. When covariates information is available, this package can make inference by incorporating the covariate information. More information can be found in the paper "Integrated Partition-Mallows Model and Its Inference for Rank Aggregation". The paper is not yet published.
Depends: R (>= 3.1.0), PerMallows, mc2d, stats
Packaged: 2020-01-09 22:11:11 UTC; wanchuangzhu