signifinder
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 7 committers (14.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.6%) to scientific vocabulary
Keywords from Contributors
bioconductor-package
gene
grna-sequence
immune-repertoire
bioinformatics
pathway-analysis
mirror
ontology
Last synced: 11 months ago
·
JSON representation
Repository
Basic Info
- Host: GitHub
- Owner: CaluraLab
- Language: R
- Default Branch: main
- Size: 22 MB
Statistics
- Stars: 8
- Watchers: 1
- Forks: 0
- Open Issues: 1
- Releases: 0
Created about 4 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
README.Rmd
---
title: "signifinder R package"
output:
github_document:
toc: false
toc_depth: 2
fig_width: 5
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
`signifinder` is an R package that collects and implements 53 expression-based signatures from cancer literature. Through the analysis of expression data with the collected signatures, `signifinder` can attribute to each sample a score per signature that summarizes many different tumor aspects, such as predict the response to therapy or the survival association, as well as quantify multiple microenvironmental conditions, such as hypoxia or the activity of the immune response.
The `signifinder` package is available from [Bioconductor](https://bioconductor.org/packages/release/bioc/html/signifinder.html), where a vignette containing examples and documentation is included.
## Installation
The `signifinder` package can be installed from Bioconductor:
```{r eval=FALSE}
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("signifinder")
```
Owner
- Name: Calura Lab
- Login: CaluraLab
- Kind: organization
- Email: enrica.calura@unipd.it
- Location: Department of Biology, University of Padova, Italy
- Website: https://www.biologia.unipd.it/people/?tx_wfqbe_pi1[account]=enrica-calura
- Twitter: CaluraEnrica
- Repositories: 2
- Profile: https://github.com/CaluraLab
Computational Cancer Genomics
GitHub Events
Total
- Watch event: 2
- Push event: 3
Last Year
- Watch event: 2
- Push event: 3
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Stefania Pirrotta | s****p@g****m | 229 |
| Fabiola Pedrini | f****i@s****t | 60 |
| Laura Masatti | l****a@l****t | 27 |
| Enrica Calura | e****a@g****m | 6 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
| Stefania Pirrotta | 1****a | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 4,764 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: signifinder
Collection and implementation of public transcriptional cancer signatures
- Homepage: https://github.com/CaluraLab/signifinder
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/signifinder/inst/doc/signifinder.pdf
- License: AGPL-3
-
Latest release: 1.10.0
published about 1 year ago
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 19.5%
Forks count: 19.8%
Average: 26.8%
Downloads: 94.7%
Maintainers (1)
Last synced:
11 months ago
Dependencies
DESCRIPTION
cran
- R >= 4.2.0 depends
- AnnotationDbi * imports
- BiocGenerics * imports
- ComplexHeatmap * imports
- DGEobj.utils * imports
- GSVA * imports
- IRanges * imports
- SummarizedExperiment * imports
- TxDb.Hsapiens.UCSC.hg19.knownGene * imports
- TxDb.Hsapiens.UCSC.hg38.knownGene * imports
- consensusOV * imports
- dplyr * imports
- ensembldb * imports
- ggplot2 * imports
- ggridges * imports
- grid * imports
- magrittr * imports
- matrixStats * imports
- maxstat * imports
- methods * imports
- openair * imports
- org.Hs.eg.db * imports
- parallel * imports
- patchwork * imports
- stats * imports
- survival * imports
- survminer * imports
- viridis * imports
- BiocStyle * suggests
- edgeR * suggests
- knitr * suggests
- limma * suggests
- testthat >= 3.0.0 suggests