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Methods to generate random gene-gene association networks and simulate RNA-seq data from them, as described in Grimes and Datta (2021) <doi:10.18637/jss.v098.i12>. Includes functions to generate random networks of any size and perturb them to obtain differential networks. Network objects are built from individual, overlapping modules that represent pathways. The resulting network has various topological properties that are characteristic of gene regulatory networks. RNA-seq data can be generated such that the association among gene expression profiles reflect the underlying network. A reference RNA-seq dataset can be provided to model realistic marginal distributions. Plotting functions are available to visualize a network, compare two networks, and compare the expression of two genes across multiple networks.

copied from cf-staging / r-seqnet
Type Size Name Uploaded Downloads Labels
conda 5.1 MB | win-64/r-seqnet-1.1.3-r44h8ae3a7c_3.conda  7 months and 24 days ago 287 main
conda 5.1 MB | win-64/r-seqnet-1.1.3-r43h8ae3a7c_3.conda  7 months and 24 days ago 306 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r44h25d921d_3.conda  7 months and 24 days ago 258 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r43h25d921d_3.conda  7 months and 24 days ago 247 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r43h0d4f4ea_3.conda  7 months and 24 days ago 909 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r44h0d4f4ea_3.conda  7 months and 24 days ago 878 main
conda 5.1 MB | win-64/r-seqnet-1.1.3-r41ha856d6a_2.conda  1 year and 9 months ago 484 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r42hac7d2d5_2.conda  1 year and 9 months ago 266 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r43hac7d2d5_2.conda  1 year and 9 months ago 269 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r42ha503ecb_2.conda  1 year and 9 months ago 1532 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r43ha503ecb_2.conda  1 year and 9 months ago 1524 main
conda 5.1 MB | win-64/r-seqnet-1.1.3-r41ha856d6a_1.tar.bz2  2 years and 5 months ago 554 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r41h49197e3_1.tar.bz2  2 years and 5 months ago 80 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r42h49197e3_1.tar.bz2  2 years and 5 months ago 77 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r42h7525677_1.tar.bz2  2 years and 5 months ago 1828 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r41h7525677_1.tar.bz2  2 years and 5 months ago 1839 main
conda 5.2 MB | win-64/r-seqnet-1.1.3-r40ha856d6a_0.tar.bz2  2 years and 9 months ago 669 main
conda 5.1 MB | win-64/r-seqnet-1.1.3-r41ha856d6a_0.tar.bz2  2 years and 9 months ago 686 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r41h8619c4b_0.tar.bz2  2 years and 9 months ago 87 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r40h8619c4b_0.tar.bz2  2 years and 9 months ago 85 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r40h7525677_0.tar.bz2  2 years and 9 months ago 2090 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r41h7525677_0.tar.bz2  2 years and 9 months ago 2090 main

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