deconvR

The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.

https://github.com/bimsbbioinfo/deconvr

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
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codemeta.json file
Found codemeta.json file
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Found .zenodo.json file
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Committers with academic emails
1 of 7 committers (14.3%) from academic institutions
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Scientific vocabulary similarity
Low similarity (17.1%) to scientific vocabulary

Keywords

bioconductor-package deconvolution dna-methylation omics regression

Keywords from Contributors

gene ontology proteomics

Last synced: 5 months ago · JSON representation

Repository

The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.

Basic Info

Host: GitHub
Owner: BIMSBbioinfo
Language: R
Default Branch: master
Homepage:
Size: 39.8 MB

Statistics

Stars: 10
Watchers: 12
Forks: 3
Open Issues: 0
Releases: 0

Topics

bioconductor-package deconvolution dna-methylation omics regression

Created over 4 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog

deconvR : Simulation and Deconvolution of Omic Profiles

logo

The deconvR package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference signature profiles and a user-selected model (non-negative least squares,quadratic programming, support vector regression, or robust linear regression). Users can directly use their reference atlas or, create an expended version of their reference atlas using findSignatures. Additionnaly, they can also use the reference atlas provided within the package, which contains cell-type specific methylation values. Another option is to simulate bulk signatures of bulk samples using simulateCellMix. And finally, we included BSmeth2Probe function along with the Illumina Methylation EPIC B5 Manifest probe IDs, to be used to map methylation data to respective probe IDs.

Installation

The deconvR package can be installed from Bioconductor:

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

BiocManager::install("deconvR") ```

You can also install the development version of deconvR directly from Github:

r remotes::install_github("BIMSBbioinfo/deconvR")

How to Use deconvR

User who wish to expand their own reference atlas can use findSignatures function. atlas is the signature matrix to be extended and samples the new data to be added to the signature matrix. atlas and samples are compliant with the function requirements. After providing appropriate atlas format, users can create samples using simulateCellMix function. You can get more information about deconvR from here.

Owner

Name: BIMSB bioinformatics platform
Login: BIMSBbioinfo
Kind: organization
Location: Berlin, Germany

Website: bioinformatics.mdc-berlin.de
Repositories: 83
Profile: https://github.com/BIMSBbioinfo

git repositories for the platform

GitHub Events

Total

Issues event: 3
Delete event: 1
Issue comment event: 2
Push event: 4
Pull request event: 1
Pull request review event: 1
Pull request review comment event: 1
Create event: 1

Last Year

Issues event: 3
Delete event: 1
Issue comment event: 2
Push event: 4
Pull request event: 1
Pull request review event: 1
Pull request review comment event: 1
Create event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 382
Total Committers: 7
Avg Commits per committer: 54.571
Development Distribution Score (DDS): 0.531

Past Year

Commits: 48
Committers: 3
Avg Commits per committer: 16.0
Development Distribution Score (DDS): 0.063

Top Committers

Name	Email	Commits
İrem Gündüz	i**z@g**m	179
İrem Gündüz	b**2@g**m	122
Veronika	s**l@h**m	46
İrem	5****z	28
Nitesh Turaga	n**a@g**m	4
J Wokaty	j**y@s**u	2
jonasfreimuth	6****h	1

Committer Domains (Top 20 + Academic)

sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

Packages

Total packages: 1
Total downloads:
- bioconductor 9,331 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 6
Total maintainers: 1

bioconductor.org: deconvR

Simulation and Deconvolution of Omic Profiles

Homepage: https://github.com/BIMSBbioinfo/deconvR
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/deconvR/inst/doc/deconvR.pdf
License: Artistic-2.0
Latest release: 1.14.2
published 6 months ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 9,331 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 0.0%

Average: 28.7%

Downloads: 86.1%

Maintainers (1)

irembgunduz@gmail.com