dsOmics Package

Development name

dsOmics

Name of server-side packages

dsOmics

Name of client-side packages

dsOmicsClient

Date this information was late updated/checked

03/05/2022

Description of packages purpose

Omics analysis. Currently the methods being supported are:

- Differential expression analysis (RNAseq/microarray data):
  • Voom + Limma
  • DESeq2
  • edgeR
- VCF data
  • PCA of SNPs
  • HWE test
  • Allele frequencies
  • Single SNP GLM
  • GWAS
  • PRS
- PLINK

How to contact developer institution/team/individual

Yannick Marcon (yannick.marcon@obiba.org)
Xavier Escribà-Montagut (xavier.escriba@isglobal.org)
Juan Ramón González (juanr.gonzalez@isglobal.org)

Latest version

1.0.10

Type distribution licence

MIT + file LICENSE

Methods of obtaining package

CRAN Address

-

GitHub account, repository and branch/tag

https://github.com/isglobal-brge/dsOmics
https://github.com/isglobal-brge/dsOmicsClient

Web-site/ftp-site/other
Tutorial: Omics data analysis with DataSHIELD: https://rpubs.com/jrgonzalezISGlobal/tutorial_DSomics

What versions of R work with the package?

server ≥ 3.6.0
client ≥ 4.0.0

What R packages do the packages depend on?

dsOmics

resourcer
tidyverse
magrittr
resourcer (≥ 1.1.1)
dummies
Biobase
SNPRelate (≥ 1.26.0)
GENESIS
GWASTools
GenomicRanges
SummarizedExperiment
MEAL (≥ 1.22.0)
knitr
DESeq2
edgeR
dplyr
readr
wkb
Rcpp (≥ 1.0.7)

dsOmicsClient
DSI
tidyverse
metap
parallel
ggrepel

Status

The package is still a work in progress. The current version is already being used “in production” to perform analysis on ExpressionSets of the LifeCycle project. This production version is being debugged by their input.

Is the package tested?

Being tested at the moment, with some previous testing already conducted.

Is the package documented?

Yes, vignettes listed on the GitHub repository README

Has the package had a disclosure audit?
No.

Is the package suitable for deployment in the production environment? (Yes/No)

Yes although some bugs may be expected.

Does your package have features to protect the privacy of data, or does it just provide remote analysis functionality?

Yes, the results returned to the client are passed through filters or dsBase functions are used, which also have protection built to them. Nevertheless we may have missed some sensible elements, it is a work in progress.

Additional Information

-