Linnorm: Linear model and normality based transformation method (Linnorm)

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Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It transforms such datasets for parametric tests. In addition to the transformtion function, the following pipelines are implemented: 1. Cell subpopluation analysis and visualization using PCA clustering, 2. Differential expression analysis or differential peak detection using limma, 3. Highly variable gene discovery and visualization, 4. Gene correlation network analysis and visualization. 5. Hierarchical clustering and plotting. Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, Linnorm provides the RnaXSim function for the simulation of RNA-seq raw counts for the evaluation of differential expression analysis methods. RnaXSim can simulate RNA-seq dataset in Gamma, Log Normal, Negative Binomial or Poisson distributions.

Author
Shun Hang Yip <shunyip@bu.edu>, Panwen Wang <pwwang@pwwang.com>, Jean-Pierre Kocher <Kocher.JeanPierre@mayo.edu>, Pak Chung Sham <pcsham@hku.hk>, Junwen Wang <junwen@uw.edu>
Date of publication
None
Maintainer
Ken Shun Hang Yip <shunyip@bu.edu>
License
MIT + file LICENSE
Version
1.2.0
URLs

View on Bioconductor

Man pages

Islam2011
scRNA-seq data from Islam et al. 2011
LIHC
Partial RNA-seq data from TCGA LIHC (Liver Hepatocellular...
Linnorm
Linnorm Transformation Function
Linnorm.Cor
Linnorm-gene correlation network analysis.
Linnorm.HClust
Linnorm-hierarchical clustering analysis.
Linnorm.HVar
Linnorm-Hvar pipeline for highly variable gene discovery.
Linnorm.limma
Linnorm-limma pipeline for Differentially Expression Analysis
Linnorm.PCA
Linnorm-PCA Clustering pipeline for subpopulation Analysis
RnaXSim
This function simulates a RNA-seq dataset based on a given...

Files in this package

Linnorm/DESCRIPTION
Linnorm/LICENSE
Linnorm/NAMESPACE
Linnorm/R
Linnorm/R/Linnorm.Cor.R
Linnorm/R/Linnorm.HClust.R
Linnorm/R/Linnorm.HVar.R
Linnorm/R/Linnorm.PCA.R
Linnorm/R/Linnorm.R
Linnorm/R/Linnorm.limma.R
Linnorm/R/Misc.R
Linnorm/R/RnaXSim.R
Linnorm/R/data.R
Linnorm/build
Linnorm/build/vignette.rds
Linnorm/data
Linnorm/data/Islam2011.rda
Linnorm/data/LIHC.rda
Linnorm/data/datalist
Linnorm/inst
Linnorm/inst/NEWS
Linnorm/inst/doc
Linnorm/inst/doc/Linnorm_User_Manual.R
Linnorm/inst/doc/Linnorm_User_Manual.Rmd
Linnorm/inst/doc/Linnorm_User_Manual.pdf
Linnorm/man
Linnorm/man/Islam2011.Rd
Linnorm/man/LIHC.Rd
Linnorm/man/Linnorm.Cor.Rd
Linnorm/man/Linnorm.HClust.Rd
Linnorm/man/Linnorm.HVar.Rd
Linnorm/man/Linnorm.PCA.Rd
Linnorm/man/Linnorm.Rd
Linnorm/man/Linnorm.limma.Rd
Linnorm/man/RnaXSim.Rd
Linnorm/src
Linnorm/src/Makevars
Linnorm/src/Makevars.win
Linnorm/src/Misc.cpp
Linnorm/vignettes
Linnorm/vignettes/Linnorm_User_Manual.Rmd