Details
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Type:
Task
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Status: Open (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Labels:None
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Epic Link:
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Sprint:Sprint 30
Description
We should add a page in the IGB user's guide about Scripting with R since this feature is mentioned in one of the most recent IGB papers.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-140 [ 14594 ] |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Rank | Ranked lower |
| Sprint | Backlog Grooming Meeting [ 29 ] | Backlog Grooming Meeting 2 [ 30 ] |
| Sprint | Backlog Grooming Meeting 2 [ 30 ] | Sprint 22 [ 29 ] |
| Rank | Ranked lower |
| Assignee | Ivory Clabaugh [ ieclabau ] |
| Sprint | Sprint 22 [ 29 ] |
| Sprint | Sprint 23 [ 30 ] |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Fix Version/s | 8.4.2 Minor Release [ 10004 ] | |
| Fix Version/s | 8.4.0 Major Release [ 10001 ] |
| Fix Version/s | 8.4.2 Minor Release [ 10004 ] |
| Sprint | Sprint 23 [ 30 ] |
| Sprint | Sprint 24 [ 31 ] |
| Rank | Ranked higher |
| Sprint | Sprint 24 [ 31 ] |
| Sprint | Sprint 25 [ 32 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | Needs Testing [ 10002 ] |
Please proof-read for sense and make sure this generally conforms to the rules about writing for the users guide.
Then pass it to Ann or David to see if this is what they wanted.
| Assignee | Ivory Clabaugh [ ieclabau ] | Mason Meyer [ mason ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Sprint | Sprint 25 [ 32 ] |
| Sprint | Sprint 26 [ 34 ] |
| Rank | Ranked higher |
| Assignee | Mason Meyer [ mason ] | David Norris [ dcnorris ] |
IGB User's Guide -> Home -> Advanced Features -> Scripting with R (Draft)
https://wiki.transvar.org/pages/viewpage.action?pageId=37945451
I will follow up with proof reading the content of the markdown and wiki page
Bitbucket link https://bitbucket.org/lorainelab/rtoigb
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Rank | Ranked higher |
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing Blocked [ 10201 ] |
| Status | Testing Blocked [ 10201 ] | Needs Testing [ 10002 ] |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Sprint | Sprint 26 [ 34 ] |
| Sprint | Sprint 27 [ 35 ] |
| Rank | Ranked higher |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Rank | Ranked lower |
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Rank | Ranked higher |
Review Notes from Mason:
- I fixed a few minor errors such as spelling errors and I capitalized some proper nouns.
- The information found directly under the section titled "Start IGB" may be more effective if it is less of a paragraph form and in more of a list form.
- R functions such as waitForFile(), IGBfunctions.R, etc. should use bold formatting since this is exact text that can be seen in R.
- I would change this: "Which genes in the test set have more than 3 transcripts?" to something similar to "Use the code below to see genes in the test set that have more than 3 transcripts." (Changed a question into an instruction)
- Some of the instructions above the code blocks seem to be telling the user to do something. I am wondering if these instructions are telling the user that they have to do something to accomplish the overall task or if these instructions are telling the user that they can follow these instructions if they have a need for it. Basically, I am wondering if the blocks of code are supposed to be performed in a specific order or if these are just code snippets that can be used at any time in a user's workflow to perform a small task. Maybe you can find a way to make this clearer, or maybe I am not understanding something.
I am reassigning this story to Ivory to make changes based on my review if she is able to or agrees with my comments.
| Status | Testing In Progress [ 10003 ] | In Progress [ 3 ] |
| Assignee | Mason Meyer [ mason ] | Ivory Clabaugh [ ieclabau ] |
| Assignee | Ivory Clabaugh [ ieclabau ] | Ann Loraine [ aloraine ] |
| Sprint | Sprint 27 [ 35 ] |
| Sprint | Sprint 28 [ 36 ] |
| Rank | Ranked higher |
| Sprint | Sprint 28 [ 36 ] | Backlog Grooming [ 37 ] |
| Sprint | Backlog Grooming [ 37 ] | Backlog Grooming 2 [ 38 ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
This needs to be reviewed before it is made public.