Package: Linnorm 2.31.0
Shun Hang Yip
Linnorm: Linear model and normality based normalization and transformation method (Linnorm)
Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods (https://doi.org/10.1038/s41592-019-0425-8). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM.
Authors:
Linnorm_2.31.0.tar.gz
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Linnorm.pdf |Linnorm.html✨
Linnorm/json (API)
NEWS
| # Install 'Linnorm' in R: |
| install.packages('Linnorm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Linnorm-2.31.0(bioc 3.21)Linnorm-2.30.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysequencingchipseqrnaseqdifferentialexpressiongeneexpressiongeneticsnormalizationsoftwaretranscriptionbatcheffectpeakdetectionclusteringnetworksinglecellcpp
Last updated 2 months agofrom:5c4a716485. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 19 2024 |
| R-4.3-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.3-mac-x86_64 | NOTE | Dec 19 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 19 2024 |
Exports:LinearRegressionLinearRegressionFPLinnormLinnorm.CorLinnorm.DataImputLinnorm.HClustLinnorm.HVarLinnorm.limmaLinnorm.NormLinnorm.PCALinnorm.SGenesLinnorm.tSNERnaXSim
Dependencies:amapapclusterclasscliclustercolorspacecpp11DEoptimRdiptestellipsefansifarverfastclusterflexmixfpcgdataggdendroggplot2gluegmodelsgtablegtoolsigraphisobandkernlablabelinglatticelifecyclelimmamagrittrMASSMatrixmclustmgcvmodeltoolsmunsellnlmennetpermutepillarpkgconfigprabclusR6RColorBrewerRcppRcppArmadillorlangrobustbaseRtsnescalesstatmodtibbleutf8vctrsveganviridisLitewithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| scRNA-seq data from Islam et al. 2011 | Islam2011 |
| Partial RNA-seq data from TCGA LIHC (Liver Hepatocellular Carcinoma) | LIHC |
| One Pass Linear Regression. | LinearRegression |
| One Pass Linear Regression with fixed point. | LinearRegressionFP |
| Linnorm Normalizing Transformation Function | Linnorm |
| Linnorm-gene correlation network analysis. | Linnorm.Cor |
| Linnorm Data Imputation Function. (In development) | Linnorm.DataImput |
| Linnorm-hierarchical clustering analysis. | Linnorm.HClust |
| Linnorm-Hvar pipeline for highly variable gene discovery. | Linnorm.HVar |
| Linnorm-limma pipeline for Differentially Expression Analysis | Linnorm.limma |
| Linnorm Normalization Function | Linnorm.Norm |
| Linnorm-PCA Clustering pipeline for subpopulation Analysis | Linnorm.PCA |
| Linnorm model stable gene selection tool. | Linnorm.SGenes |
| Linnorm t-SNE Clustering pipeline for subpopulation Analysis | Linnorm.tSNE |
| This function simulates an RNA-seq dataset based on a given distribution. | RnaXSim |
| Partial RNA-seq data from SEQC/MAQC-III Sample A | SEQC |
