https://github.com/cbg-ethz/mnem
Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem
Science Score: 57.0%
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Found 2 DOI reference(s) in README -
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Low similarity (6.7%) to scientific vocabulary
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Repository
Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- Language: R
- Default Branch: master
- Homepage: https://bioconductor.org/packages/mnem
- Size: 27.2 MB
Statistics
- Stars: 4
- Watchers: 3
- Forks: 3
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
M&NEM
Single cell RNA-seq data sets from pooled CrispR screens provide the possibility to analyzse hete rogeneous cell populations. We extended the original Nested Effects Models (NEM) to Mixture Nested Effects Models (M&NEM) to simulataneously identify several causal signalling graphs and corresponding subpopulations of cells. The final result will be a soft clustering of the perturbed cells and a causal signalling graph, which describes the interactions of the perturbed genens for each cluster of cells.
Install:
```{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("mnem") ```
Most recent (devel) version:
```{r} install.packages("devtools")
library(devtools)
install_github("cbg-ethz/mnem")
library(mnem) ```
Small toy example with five S-genes and 1000 simulated cells. Each S-gene has two E-genes. The two components have weights 40 and 60 percent. The simulated data set consists of log ratios for effects (1) and no effects (-1). We add Gaussian noise with mean 0 and standard deviation 1. We learn an optimum with components set to two and ten random starts for the EM algorithm.
{r}
sim <- simData(Sgenes = 5, Egenes = 2, Nems = 2, mw = c(0.4,0.6))
data <- (sim$data - 0.5)/0.5
data <- data + rnorm(length(data), 0, 1)
result <- mnem(data, k = 2, starts = 10)
plot(result)
For the reproduction of the publication see the scripts in the other directory.
References:
Pirkl, M., Beerenwinkel, N.; Single cell network analysis with a mixture of Nested Effects Models, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i964-i971, https://doi.org/10.1093/bioinformatics/bty602.
Owner
- Name: Computational Biology Group (CBG)
- Login: cbg-ethz
- Kind: organization
- Location: Basel, Switzerland
- Website: https://www.bsse.ethz.ch/cbg
- Twitter: cbg_ethz
- Repositories: 91
- Profile: https://github.com/cbg-ethz
Beerenwinkel Lab at ETH Zurich
GitHub Events
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- Push event: 7
Last Year
- Push event: 7
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| MartinFXP | m****l@b****h | 234 |
| mpirkl | m****l@y****e | 25 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 10 |
| viktoria023 | 6****3 | 3 |
Committer Domains (Top 20 + Academic)
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Last synced: 6 months ago
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- Total issues: 1
- Total pull requests: 1
- Average time to close issues: about 1 month
- Average time to close pull requests: 3 days
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
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Top Authors
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- bitmask (1)
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- viktoria023 (1)
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- Total packages: 1
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Total downloads:
- bioconductor 13,523 total
- Total dependent packages: 4
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: mnem
Mixture Nested Effects Models
- Homepage: https://github.com/cbg-ethz/mnem/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/mnem/inst/doc/mnem.pdf
- License: GPL-3
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Latest release: 1.24.0
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1 depends
- Linnorm * imports
- Rcpp * imports
- RcppEigen * imports
- Rgraphviz * imports
- cluster * imports
- data.table * imports
- e1071 * imports
- flexclust * imports
- ggplot2 * imports
- grDevices * imports
- graph * imports
- graphics * imports
- lattice * imports
- matrixStats * imports
- methods * imports
- naturalsort * imports
- snowfall * imports
- stats * imports
- stats4 * imports
- tsne * imports
- utils * imports
- wesanderson * imports
- BiocGenerics * suggests
- RUnit * suggests
- devtools * suggests
- epiNEM * suggests
- knitr * suggests
- rmarkdown * suggests