Package: MetaNet 0.2.1

MetaNet: Network Analysis for Omics Data

Comprehensive network analysis package. Calculate correlation network fastly, accelerate lots of analysis by parallel computing. Support for multi-omics data, search sub-nets fluently. Handle bigger data, more than 10,000 nodes in each omics. Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize. Provide comprehensive topology indexes calculation, including ecological network stability.

Authors:Chen Peng [aut, cre]

MetaNet_0.2.1.tar.gz
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MetaNet.pdf |MetaNet.html✨
MetaNet/json (API)
NEWS

# Install 'MetaNet' in R:
install.packages('MetaNet', repos = c('https://asa12138.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/asa12138/metanet/issues

Datasets:

On CRAN:

dataimportnetwork analysisomicssoftwarevisualization

5.66 score 13 stars 8 scripts 181 downloads 90 exports 43 dependencies

Last updated 4 months agofrom:dea2e92ba0. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winERRORNov 14 2024
R-4.5-linuxERRORNov 14 2024
R-4.4-winERRORNov 14 2024
R-4.4-macERRORNov 14 2024
R-4.3-winERRORNov 14 2024
R-4.3-macERRORNov 14 2024

Exports:%<>%%>%anno_edgeanno_vertexas_arcas_circle_treeas_lineas_polyarcas_polycircleas_polygonas.ggigas.metanetc_net_annotatec_net_buildc_net_calc_net_calculatec_net_filterc_net_from_edgelistc_net_indexc_net_layc_net_layoutc_net_loadc_net_modulec_net_plotc_net_savec_net_setc_net_stabilityc_net_unionc_net_updatecal_simcheck_tabsclean_igraphclean_multi_edge_metanetCohesioncombine_n_modulecompare_randdf2net_treeextract_sample_netfast_corfilter_n_modulefit_powerg_layoutg_layout_backboneg_layout_circlepackg_layout_niceg_layout_polyarcg_layout_polycircleg_layout_polygong_layout_stressg_layout_treemapget_communityget_eget_group_skeletonget_moduleget_module_eigenget_nget_vinput_gephiis_metanetlinks_statmodule_detectmodule_eigenmodule_expressionmodule_netmulti_net_buildncnet_parnetD3plotolympic_rings_netp.adjust.tableplot_module_treerand_netrand_net_parread_corrrmtRMT_thresholdrobust_testrobustnesssave_corrshow_MetaNet_logoskeleton_plotsmallworldnesssumm_2colsummary_moduleto_module_nettwocol_edgelistvenn_netvulnerabilityzp_analysezp_plot

Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggnewscaleggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepcutilspillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

MetaNet: Network Analysis for Omics Data

Chen Peng

Rendered fromMetaNet.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-03-21
Started: 2023-06-25

Readme and manuals

Help Manual

Help pageTopics
Use dataframe to annotate edges of an igraphanno_edge
Use data.frame to annotate vertexes of metanetanno_node anno_vertex
Edgelistarc_count
Edgelistarc_taxonomy
Layout as a arcas_arc
Layout as a circle_treeas_circle_tree
Layout as a lineas_line
Layout as a polyarcas_polyarc
Layout as a polycircleas_polycircle
Layout as a polygonas_polygon
Transfer an igraph object to a ggigas.ggig
Annotate a metanetc_net_annotate
Construct a metanet from a corr objectc_net_build
Calculate correlation for one or two t(otutab), or distance for one t(otutab).c_net_cal c_net_calculate
Filter a network according to some attributesc_net_filter
Construct a network from edge_list dataframec_net_from_edgelist
Layout coordinatesc_net_lay c_net_layout
Load network filec_net_load
Plot a metanetc_net_plot
Save network filec_net_save
Set basic attributes from totu tablec_net_set
Evaluate the stability of a networkc_net_stability robustness robust_test vulnerability
Union two networksc_net_union
Update a metanet object or transform igraph object to metanet objectas.metanet c_net_update
Calculate similarity for one t(otutab)cal_sim
Check tables and extract common samplescheck_tabs
Clean a igraph objectclean_igraph
Clean multi edge metanet to plotclean_multi_edge_metanet
MetaNet networksco_net
MetaNet networksco_net_rmt
MetaNet networksco_net2
Cohesion calculationCohesion plot.cohesion
Transform a dataframe to a network edgelist.df2net_tree
Extract each sample network from the whole networkextract_sample_net
Fast correlation calculationfast_cor
Filter some modules as otherscombine_n_module filter_n_module plot_module_tree
Fit power-law distribution for an igraphfit_power
Layout with groupg_layout
Layout with group nicelyg_layout_backbone g_layout_circlepack g_layout_nice g_layout_stress g_layout_treemap
Layout with group as a polygong_layout_polyarc g_layout_polycircle g_layout_polygon
Get communityget_community
Get edge informationget_e
Get skeleton network according to a groupget_group_skeleton skeleton_plot
Get moduleget_module
Get module_eigenget_module_eigen
Get network informationget_n
Get vertex informationget_v
Input a graphml file exported by Gephiinput_gephi
Is this object a metanet object?is.metanet is_metanet
Link summary of the networklinks_stat
MetaNet networks abundancemetab
MetaNet networks metadatametab_g
MetaNet networks abundancemicro
MetaNet networks metadatamicro_g
Detect the modulesc_net_module module_detect
Calculate the eigenvalue of each module and correlation of nodes and eigenvalue (node_eigen_cor).module_eigen module_expression
Generate a n-modules networkmodule_net
Multi-omics network buildmulti_net_build
MetaNet networksmulti1
Calculate natural_connectivitync
Calculate all topological indexes of a networkc_net_index net_par
plot use networkD3netD3plot
Plot olympic rings using networkolympic_rings_net
p.adjust apply on a correlation table (matrix or data.frame)p.adjust.table
Plot a ggigplot.ggig
Plot a metanetplot.metanet
Plot a rmt_resplot.rmt_res
Plot robustplot.robust
Plot robustnessplot.robustness
Plot vulnerabilityplot.vulnerability
Print method for 'cohesion' objectsprint.cohesion
Print method for 'coors' objectsprint.coors
Print method for 'corr' objectsprint.corr
Print method for 'ggig' objectsprint.ggig
Print method for 'metanet' objectsprint.metanet
Print method for 'robust' objectsprint.robust
Print method for 'robustness' objectsprint.robustness
Print method for 'vulnerability' objectsprint.vulnerability
Degree distribution comparison with random networkrand_net
Net_pars of many random networkcompare_rand rand_net_par
Read a corr objectread_corr
Get RMT threshold for a correlation matrixrmt RMT_threshold
Save a corr objectsave_corr
Show MetaNet logoshow_MetaNet_logo
Calculate small-world coefficientsmallworldness
Summaries two columns informationsumm_2col
Summary module indexsummary_module
Summary method for 'corr' objectssummary.corr
Transformation a network to a module networkto_module_net
MetaNet networks abundancetransc
MetaNet networks metadatatransc_g
Quick build a metanet from two columns tabletwocol_edgelist
Venn networkvenn_net
Zi-Pi calculatezp_analyse zp_plot