Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:3
-
Sprint:Fall 2 2023 Sep 17, Fall 3 2023 Oct 2, Fall 4 2023 Oct 16
Description
Purpose: Write a first draft of an EB-Seq script to analyze the time course data.
Why? Because comparing time points violates an assumption of independence, a few tools have been developed to address this and improve the RNA-seq comparisons on time dependent studies.
A few examples:
- mfuzz
- PAL-D
- EB-Seq
I tested out PAL-D last January and it was a horrible experience.
Rasha ran mfuzz with success.
EB-Seq has been run by me and Liz in the past.
Liz's details on Eb0seq can be found here:
_Original details from Liz Cooper
“EBSeq script on my GitHub page associated with the sweet sorghum paper (in case you decide to use that package): “
Rio/EBSeqHMM_Cluster.R at master · eacooper400/Rio · GitHub
Liz_
In R:
The R package should be acquired like so:
-
-
- Installing Required Packages (only done once)
#source("https://bioconductor.org/biocLite.R")
BiocManager::install("EBSeq")
BiocManager::install("EBSeqHMM")
install.packages("blockmodeling")
- Installing Required Packages (only done once)
-
-
-
- Load Required Pacakges
library(EBSeq)
library(EBSeqHMM)
- Load Required Pacakges
-
Attachments
Issue Links
- is blocked by
-
-
- Closed
-