Introduction | Installation | Data description | Finding motifs | PPI V | V | Lambda | Delta | Bifan | Counting motifs and evaluating significance | Evaluting interaction similarity | Session information | References
Package: magrene 1.15.0
Fabrício Almeida-Silva
magrene: Motif Analysis In Gene Regulatory Networks
magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index.
Authors:
magrene_1.15.0.tar.gz
magrene_1.15.0.zip(r-4.7)magrene_1.15.0.zip(r-4.6)magrene_1.15.0.zip(r-4.5)
magrene_1.15.0.tgz(r-4.6-any)magrene_1.15.0.tgz(r-4.5-any)
magrene_1.15.0.tar.gz(r-4.7-any)magrene_1.15.0.tar.gz(r-4.6-any)
magrene_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
magrene/json (API)
| # Install 'magrene' in R: |
| install.packages('magrene', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/almeidasilvaf/magrene/issues
Datasets:
- gma_grn - Sample soybean GRN
- gma_paralogs - Soybean (Glycine max) duplicated genes
- gma_ppi - Sample soybean PPI network
- nulls - Null distribution of motif frequencies for vignette data set
On BioConductor:magrene-1.15.0(bioc 3.24)magrene-1.14.0(bioc 3.23)
softwaremotifdiscoverynetworkenrichmentsystemsbiologygraphandnetworkgene-regulatory-networkmotif-analysisnetwork-motifsnetwork-science
Last updated from:b2761b4207. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 164 | ||
| linux-devel-x86_64 | NOTE | 220 | ||
| source / vignettes | OK | 224 | ||
| linux-release-x86_64 | NOTE | 220 | ||
| macos-release-arm64 | NOTE | 103 | ||
| macos-oldrel-arm64 | NOTE | 103 | ||
| windows-devel | NOTE | 123 | ||
| windows-release | NOTE | 116 | ||
| windows-oldrel | NOTE | 115 | ||
| wasm-release | OK | 120 |
Exports:calculate_Zfind_bifanfind_deltafind_lambdafind_ppi_vfind_vgenerate_nullssd_similarity
Dependencies:BHBiocParallelcodetoolscpp11formatRfutile.loggerfutile.optionslambda.rsnow
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate Z-score for motif frequencies | calculate_Z |
| Find bifan motifs | find_bifan |
| Find delta motifs | find_delta |
| Find lambda motifs | find_lambda |
| Find V motifs in protein-protein interactions | find_ppi_v |
| Find V motifs | find_v |
| Generate null distributions of motif counts for each motif type | generate_nulls |
| Sample soybean GRN | gma_grn |
| Soybean (Glycine max) duplicated genes | gma_paralogs |
| Sample soybean PPI network | gma_ppi |
| Null distribution of motif frequencies for vignette data set | nulls |
| Calculate Sorensen-Dice similarity between paralogous gene pairs | sd_similarity |
