Compare Clusters Workflow
- Jen Garbarino |
- 14 steps |
- 2 minutes
Compare clusters workflow is a downstream analysis to compare combinations of clusters between conditions. Input the combination of clusters you would like to compare and it will output the differential gene, peaks and motifs for that combination.
1
Click on the workflows button in LatchBio to go to the workflows tab
2
Click on the comapre clusters workflow
3
Enter a project name
4
Next input the ArchRProject to use for the comparison
5
Click "Select Folder" and navigate to the folder containing the ArchRProject you wish to analyze. Make sure to find the file containing the ArchRProject (named Save-ArchR-Project.rds) within the data folder.Click "Select"
6
Click add row to add a grouping
7
Input the Clusters you wish to compare with a dash or separated by columns.
Example: C1, C2, C3-C5 will work
cluster1 cluster3 to 6 would not work
Grouping rules are also available in the about page of the workflow
8
Input the condition for these clusters
Make sure the condition spelling and captialization matches the conditions in the data (go to the medians.csv table to see the conditions used)
9
If you have multiple conditions in your data, turn this on to have all samples in that condition included.
Example:
- Sample1: young-control
- Sample2: young-experiment
- Sample3: old-control
- Sample4: old-experiment
To select cells from Sample1 and Sample2, enter “young” into the Condition field and set the Multiple button to True (on). Otherwise, Sample1 and Sample2 must be specified by entering “young-control,young-experiment” into the Condition field.
10
Next input the second set of clusters you wish to compare
11
Input the condition for these clusters
Cluster cannot be contained within both groups:
Example C1-C4 vs C3-C6 will not work
12
If multiple conditions, turn this on. Follow same rules from step 9
13
Select genome for project
14
Click Launch Workflow to start the workflow
