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
- Differential expression analysis (RNAseq/microarray data):
- Voom + Limma
- DESeq2
- edgeR
- PCA of SNPs
- HWE test
- Allele frequencies
- Single SNP GLM
- GWAS
- PRS
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
-
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)
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.
Being tested at the moment, with some previous testing already conducted.
Yes, vignettes listed on the GitHub repository README
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.