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bvieth / powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
https://bvieth.github.io/powsimR/
Artistic License 2.0
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Dependency Issue #47

Closed WXNCjlopez closed 3 years ago

WXNCjlopez commented 4 years ago

Hi, the Bioconductor package "DEDS" is required, but as mentioned in

https://bioconductor.org/packages/release/bioc/html/DEDS.html

the package is deprecated. Is there anything I can if I am using R version 4.0? Thank you.

newbi-pvh commented 4 years ago

I am experiencing the same problem. I am holding off installing powsimR until I can resolve this issue.

cellsera commented 4 years ago

Same deal; I am unable to install powsimR due to the unavailability of DEDS.

newbi-pvh commented 4 years ago

I ran thru a couple rounds of updating other dependencies and biocparalell. DEDS finally installed but now another issue when installing powsimr.

Good luck! Pam

Sent from my iPhone

On Jun 12, 2020, at 12:39 PM, cellsera notifications@github.com wrote:

 Same deal; I am unable to install powsimR due to the unavailability of DEDS.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

bvieth commented 4 years ago

Hello,

I am sorry that you have encountered this issue. I have updated powsimR to be compatible with the newest Bioconductor release (MAST had some name changes of functions and DEDS is deprecated). I hope you will give it another go.

Feel free to contact me again.

Best Beate

newbi-pvh commented 4 years ago

Wow! thank you so much for your response. I will give it another try.

Best Regards,

Pam

On Jun 18, 2020, at 9:26 AM, Beate Vieth notifications@github.com wrote:

Hello,

I am sorry that you have encountered this issue. I have updated powsimR to be compatible with the newest Bioconductor release (MAST had some name changes of functions and DEDS is deprecated). I hope you will give it another go.

Feel free to contact me again.

Best Beate

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bvieth/powsimR/issues/47#issuecomment-646143301, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP3LDL5XSEQLZNJ5RNQEWYDRXI52FANCNFSM4NEXHAVQ.

WXNCjlopez commented 3 years ago

Hi Beate, I got it running, thank you for your prompt response. Jose.