Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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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:
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- 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)
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- Load Required Pacakges
library(EBSeq)
library(EBSeqHMM)
- Load Required Pacakges
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Attachments
Issue Links
- is blocked by
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3446 [ 22548 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | journal.pone.0264246.pdf [ 17962 ] |
| Sprint | Fall 2 2023 Sep 17 [ 178 ] | Fall 2 2023 Sep 17, Fall 3 2023 Oct 2 [ 178, 179 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | masterTable-ebseqhmm.xlsx [ 18054 ] |
| Sprint | Fall 2 2023 Sep 17, Fall 3 2023 Oct 2 [ 178, 179 ] | Fall 2 2023 Sep 17, Fall 3 2023 Oct 2, Fall 4 2023 Oct 16 [ 178, 179, 180 ] |
| Rank | Ranked higher |
| Attachment | RNAseq_fnxs.R [ 18061 ] | |
| Attachment | muday-144-SL4_counts-salmon.txt [ 18062 ] | |
| Attachment | Ebseq-hmm_mudayTimeCourse-Version2 2.R [ 18063 ] |
| Attachment | Ebseq-hmm_mudayTimeCourse-Version2.R [ 18065 ] | |
| Attachment | muday-144-SL4_counts-salmon.txt [ 18066 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] |
| Assignee | Molly Davis [ molly ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Molly Davis [ molly ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Robert Reid [ robertreid ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Ebseq-hmm_mudayTimeCourse-Version3.R [ 18076 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Molly Davis [ molly ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Robert Reid [ robertreid ] |