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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 14 days ago 283 main
conda 5.1 MB | win-64/r-seqnet-1.1.3-r43h8ae3a7c_3.conda  7 months and 14 days ago 302 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r44h25d921d_3.conda  7 months and 14 days ago 257 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r43h25d921d_3.conda  7 months and 14 days ago 244 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r43h0d4f4ea_3.conda  7 months and 14 days ago 886 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r44h0d4f4ea_3.conda  7 months and 14 days ago 855 main
conda 5.1 MB | win-64/r-seqnet-1.1.3-r41ha856d6a_2.conda  1 year and 9 months ago 482 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 268 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r42ha503ecb_2.conda  1 year and 9 months ago 1510 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r43ha503ecb_2.conda  1 year and 9 months ago 1497 main
conda 5.1 MB | win-64/r-seqnet-1.1.3-r41ha856d6a_1.tar.bz2  2 years and 5 months ago 552 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r41h49197e3_1.tar.bz2  2 years and 5 months ago 79 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r42h49197e3_1.tar.bz2  2 years and 5 months ago 76 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r42h7525677_1.tar.bz2  2 years and 5 months ago 1805 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r41h7525677_1.tar.bz2  2 years and 5 months ago 1816 main
conda 5.2 MB | win-64/r-seqnet-1.1.3-r40ha856d6a_0.tar.bz2  2 years and 9 months ago 668 main
conda 5.1 MB | win-64/r-seqnet-1.1.3-r41ha856d6a_0.tar.bz2  2 years and 9 months ago 685 main
conda 5.1 MB | osx-64/r-seqnet-1.1.3-r41h8619c4b_0.tar.bz2  2 years and 9 months ago 86 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 2064 main
conda 5.1 MB | linux-64/r-seqnet-1.1.3-r41h7525677_0.tar.bz2  2 years and 9 months ago 2065 main

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