diff --git a/README.md b/README.md index 0008d91..2864216 100644 --- a/README.md +++ b/README.md @@ -385,51 +385,8 @@ SRR1234567 <- limiric(

-##### 3. Combine ```limiric``` annotations with ```DropletQC``` -Detect damaged cells and compare results with those from ```DropletQC```. - -```R -SRR1234567 <- limiric( - project_name = "SRR1234567", - filtered_path = "/home/user/alignment/SRR1234567/filtered/", - droplet_qc = TRUE, - velocyto_path = "/home/user/alignment/velocyto/", - output_path = "/home/user/alignment/limiric/" -) -``` -> **NB** This will change your output directory structure by adding a new ```DropletQC``` layer -> -> ``` -> output_path/ -> ├── CellQC -> | -> ├── DropletQC -> | -> ├── RBCQC -> | -> └── Filtered -> ``` -> - -
- - - - - - -
- This will output a scatter plot and tSNE showing the cells annotated as damaged by both limiric and DropletQC. - - Scatter plot -
- - - -
- -##### 4. Combine previous condition -Perform ambient RNA correction with ```SoupX```, filter red blood cells, isolate immune cells, detect damaged cells, and compare against ```DropletQC```. +##### 3. Combine previous condition +Perform ambient RNA correction with ```SoupX```, filter red blood cells, isolate immune cells and detect damaged cells. ```R SRR1234567 <- limiric( @@ -437,7 +394,6 @@ SRR1234567 <- limiric( filtered_path = "/home/user/alignment/SRR1234567/filtered/", soupx = TRUE, raw_path = "/home/user/alignment/SRR1234567/raw/", - droplet_qc = TRUE, isolate_cd45 = TRUE, velocyto_path = "/home/user/alignment/velocyto/", output_path = "/home/user/alignment/limiric/" @@ -450,8 +406,6 @@ SRR1234567 <- limiric( > > ├── CellQC > | -> ├── DropletQC -> | > ├── IMCQC > | > ├── RBCQC