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bnem

Boolean Nested Effect Models - https://doi.org/10.1093/bioinformatics/btv680 - https://bioconductor.org/packages/bnem

https://github.com/martinfxp/bnem

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
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    Committers with academic emails
    3 of 6 committers (50.0%) from academic institutions
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics ontology sequencing proteomics
Last synced: 10 months ago · JSON representation

Repository

Boolean Nested Effect Models - https://doi.org/10.1093/bioinformatics/btv680 - https://bioconductor.org/packages/bnem

Basic Info
  • Host: GitHub
  • Owner: MartinFXP
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 4.87 MB
Statistics
  • Stars: 2
  • Watchers: 0
  • Forks: 1
  • Open Issues: 3
  • Releases: 0
Created about 11 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

B-NEM

Boolean Nested Effects Models (B-NEM) are used to infer signalling pathways. In different experiments (conditions) members of a pathway (S-genes) are stimulated or inhibited, alone and in combination. In each experiment transcriptional targets (E-genes) of the pathway react differently and are higher or lower expressed depending on the condition. From these differential expression profiles B-NEM infers Boolean functions presented as hyper-edges of a hyper-graph connecting parents and children in the pathway. For example if the signal is transducted by two parents A and B to a child C and the signal can be blocked with a knock-down of either one, they are connected by a typical AND-gate. If the signal is still transduced during a single knock-down, but blocked by the double knock-down of A and B, they activate C by an OR-gate. In general the state of child C is defined by a Boolean function

f: {0,1}^n -> {0,1}, C = f(A1, ... , An)

with its parents A_i, i ∈ {1,...,n}.

Install:

```{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("bnem") ```

Most recent (devel) version:

```r install.packages("devtools")

library(devtools)

install_github("MartinFXP/bnem")

library(bnem) ```

Then check out the vignette for working examples.

r vignette("bnem")

Publication result:

Use the function ?processDataBCR to reproduce the data analysed in the publication (Pirkl et. al., 2016).

References:

Pirkl, Martin, Hand, Elisabeth, Kube, Dieter, & Spang, Rainer. 2016. Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models. \textit{Bioinformatics}, 32(6), 893–900.

Pirkl, Martin. 2016. Indirect inference of synergistic and alternative signalling of intracellular pathways. University of Regensburg.

Owner

  • Login: MartinFXP
  • Kind: user

GitHub Events

Total
  • Push event: 3
Last Year
  • Push event: 3

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 172
  • Total Committers: 6
  • Avg Commits per committer: 28.667
  • Development Distribution Score (DDS): 0.442
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
MartinFXP m****l@b****h 96
MartinFXP m****l@u****e 43
mpirkl m****l@y****e 11
J Wokaty j****y@s****u 10
Nitesh Turaga n****a@g****m 6
MartinFXP m****l@b****h 6
Committer Domains (Top 20 + Academic)
bs-mbpr189.d.ethz.ch: 1 sph.cuny.edu: 1 yahoo.de: 1 ukr.de: 1 bsse.ethz.ch: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 10
  • Total pull requests: 0
  • Average time to close issues: 10 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.2
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MartinFXP (10)
Pull Request Authors
Top Labels
Issue Labels
enhancement (4) bug (3) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 7,521 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: bnem

Training of logical models from indirect measurements of perturbation experiments

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 7,521 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 18.4%
Stargazers count: 21.8%
Average: 24.6%
Downloads: 83.0%
Maintainers (1)
martinpirkl@yahoo.de
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • Biobase * imports
  • CellNOptR * imports
  • RColorBrewer * imports
  • Rgraphviz * imports
  • affy * imports
  • binom * imports
  • cluster * imports
  • epiNEM * imports
  • flexclust * imports
  • graph * imports
  • graphics * imports
  • limma * imports
  • matrixStats * imports
  • methods * imports
  • mnem * imports
  • rmarkdown * imports
  • snowfall * imports
  • stats * imports
  • sva * imports
  • utils * imports
  • vsn * imports
  • BiocGenerics * suggests
  • knitr * suggests