Packaged: 2019-12-20 06:36:20 UTC; thongpham

Packaged: 2020-01-08 10:59:24 UTC; thongpham

Packaged: 2020-02-06 16:07:38 UTC; thongpham

Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>.
Packaged: 2020-02-17 03:53:48 UTC; thongpham

Packaged: 2021-05-17 02:09:13 UTC; thongpham

Packaged: 2021-07-22 15:11:34 UTC; thongpham

Packaged: 2021-05-12 16:35:47 UTC; thongpham

Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>. Thong Pham et al. (2021) <doi:10.1093/comnet/cnab024>.
Packaged: 2021-10-29 15:10:06 UTC; thongpham

Packaged: 2022-01-11 05:26:48 UTC; thongpham

Title: Pairwise Association of Functional Annotations
Authors@R: c(person(given = "Daphne", family = "Ezer", role = c("aut", "cre"), email="daphne.ezer@york.ac.uk"),
person(given = "Mahair", family = "Mahjoub", role = c("aut"), email="mahiarmahjoub@gmail.com"))
Description: Finds pairs of functional annotations or gene ontology (GO)
terms that are enriched within a directed network (such as a gene
regulatory network).  This works with or without edge weights and
includes visualizations (both as a network where the functions are
nodes and as a heatmap).  PAFway is an acronym for Pairwise Associations of
Functional annotations in biological networks and pathWAYs.
Imports: igraph, gplots, ggplot2, GGally, network, sna, scales, stats,

Imports: igraph, ggplot2, GGally, network, sna, scales, stats,

Title: The package can identify the dysregulated KEGG pathways based on
global influence from the internal effect of pathways and
Author: Junwei Han,Yanjun Xu,Haixiu Yang,Chunquan Li and Xia Li
Description: The package can identify the dysregulated KEGG pathways
based on global influence from the internal effect of pathways
and crosstalk between pathways. (1) The PAGI package can
prioritize the pathways associated with two biological states
by statistical significance or FDR. (2) The PAGI package can
evaluated the global influence factor (GIF) score in the global
gene-gene network constructed based on the relationships of
genes extracted from each pathway in KEGG database and the
biocViews: Statistics, crosstalk, Pathways, Graphs, Networks