Data

Tools

Indexes

Applications

Experiments

Open Source Science

ingres

Inferring Probabilistic Boolean Networks of Gene Regulation Using Protein Activity Enrichment Scores

https://github.com/cbigoxf/ingres

Science Score: 13.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Inferring Probabilistic Boolean Networks of Gene Regulation Using Protein Activity Enrichment Scores

Basic Info
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created almost 5 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# ingres
[![codecov](https://codecov.io/gh/CBigOxf/ingres/branch/master/graph/badge.svg?token=XQHKMZPKEB)](https://app.codecov.io/gh/CBigOxf/ingres)
[![R-CMD-check](https://github.com/CBigOxf/ingres/workflows/R-CMD-check/badge.svg)](https://github.com/CBigOxf/ingres/actions)
[![doi](https://img.shields.io/badge/doi-10.1101/2022.09.04.506528-yellow.svg)](https://doi.org/10.1101/2022.09.04.506528)


***I**nferring Probabilistic Boolean **N**etworks of **G**ene **R**egulation Using Protein Activity **E**nrichment **S**cores*

Given a gene regulatory boolean network and a RNA-seq dataset, **ingres** computes protein activity normalised enrichment scores using VIPER, and then produces a probabilistic network using the scores as probabilities for fixed node activation or deactivation, in addition to the original boolean functions.

## Installation
You can install **ingres** from CRAN:

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

Or you can install the development version of **ingres** with:

``` r
# install.packages("devtools")
devtools::install_github("CBigOxf/ingres")
```

You may need to manually install some of the BioConductor dependencies before you can install **ingres**:


``` r
# install.packages("BiocManager")
BiocManager::install(c("viper", "AnnotationDbi", "org.Hs.eg.db", "aracne.networks"))
```

## Citation

To cite **ingres** in publications use:

| *Victori, P. & Buffa, F. M. Ingres: from single-cell RNA-seq data to single-cell probabilistic Boolean networks. 2022.09.04.506528 Preprint at  (2022).*

Owner

  • Name: CBigOxf
  • Login: CBigOxf
  • Kind: organization
  • Email: francesca.buffa@oncology.ox.ac.uk
  • Location: Oxford

GitHub Events

Total
Last Year

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 175
  • Total Committers: 2
  • Avg Commits per committer: 87.5
  • Development Distribution Score (DDS): 0.011
Top Committers
Name Email Commits
Pedro Victori f****a@g****m 173
Pedro Victori 2****i@u****m 2

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
cran.r-project.org: ingres

Infer Gene Probabilistic Boolean Networks from Single-Cell Data

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 0
Rankings
Forks count: 28.8%
Dependent packages count: 29.8%
Stargazers count: 31.7%
Dependent repos count: 35.5%
Average: 43.1%
Downloads: 89.7%
Last synced: almost 3 years ago

Dependencies

DESCRIPTION cran
  • R >= 3.6.0 depends
  • AnnotationDbi * imports
  • Seurat * imports
  • dplyr * imports
  • ggplot2 * imports
  • ggpubr * imports
  • ggraph * imports
  • igraph * imports
  • magrittr * imports
  • methods * imports
  • org.Hs.eg.db * imports
  • purrr * imports
  • readr * imports
  • rlang * imports
  • scales * imports
  • stringr * imports
  • tibble * imports
  • tidygraph * imports
  • tidyr * imports
  • tidyselect * imports
  • usethis * imports
  • viper * imports
  • BoolNet * suggests
  • aracne.networks * suggests
  • covr * suggests
  • knitr * suggests
  • plotly >= 4.10.0 suggests
  • rmarkdown * suggests
  • shiny * suggests
  • testthat >= 3.0.0 suggests
  • withr * suggests