example 6: vampseq

Author: nickzoic

docs/further-examples/img/s6_1.jpg

@@ -5,7 +5,7 @@ layout: default
 # Further Examples
 
 Continuing on from the examples in [Getting Started with CountESS](../getting-started/)
-let's look at a more realistic experiment.
+let's look at some more realistic experiments:
 
 ## Example 5: Deep Mutational Scan of BRCA1
 
@@ -107,28 +107,66 @@ before calculating scores as above:
 
 [![Screenshot 12](img/s5_12.jpg)](img/s5_12.png)
 
-[![Screenshot 13](img/s5_13.jpg)](img/s5_13.png)
+<!--[![Screenshot 13](img/s5_13.jpg)](img/s5_13.png)-->
+
+This will let us calculate scores and sigmas per
+DNA variant instead of per barcode:
 
 [![Screenshot 14](img/s5_14.jpg)](img/s5_14.png)
 
-[![Screenshot 16](img/s5_16.jpg)](img/s5_16.png)
+Scores can then be combined just like the "per barcode" 
+example:
+<!--[![Screenshot 16](img/s5_16.jpg)](img/s5_16.png)-->
 
 [![Screenshot 17](img/s5_17.jpg)](img/s5_17.png)
 
 ### Scoring by Protein
 
-... Or to collate by protein variant:
+... Or we can collate by protein variant:
 
 [![Screenshot 21](img/s5_21.jpg)](img/s5_21.png)
 
-[![Screenshot 22](img/s5_22.jpg)](img/s5_22.png)
+<!--[![Screenshot 22](img/s5_22.jpg)](img/s5_22.png)
 
 [![Screenshot 15](img/s5_15.jpg)](img/s5_15.png)
 
-[![Screenshot 18](img/s5_18.jpg)](img/s5_18.png)
+[![Screenshot 18](img/s5_18.jpg)](img/s5_18.png)-->
 
 [![Screenshot 19](img/s5_19.jpg)](img/s5_19.png)
 
 
+### Other Options
+
+The above example uses two replicates and three time points.
+If only two timepoints are available, the scoring plugin falls
+back on the "log ratio" version of the scoring formula, also
+as per Enrich2.
+
+If there's no suitable "wild type indicator" column, the 
+scoring plugin can use the total of all variants instead, also
+as per Enrich2.
+
+## Example 6: VAMPseq
+
+[VAMP-seq](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5980760/)
+sorts cells into bins and uses a weighted sum of the frequencies of 
+variants in each bin to calculate a score for each variant.
+
+In this example we have three replicates each of which has counts in
+four bins.
+
+The first step is to load and collate these files just like in
+[Example 3](../getting-started/#example-3):
+
+[![Screenshot 1](img/s6_1.jpg)](img/s6_1.png)
+
+Then we can use the [VAMPseq Plugin](../included-plugins/#vampseq) to calculate scores
+for each variant:
+
+[![Screenshot 2](img/s6_2.jpg)](img/s6_2.png)
 
+Once that's done, pivot on replicate and use a simple formula to combine scores
+into an average score and an estimated standard deviation:
 
+[![Screenshot 3](img/s6_3.jpg)](img/s6_3.png)
+[![Screenshot 4](img/s6_4.jpg)](img/s6_4.png)

docs/further-examples/img/s6_1.png

@@ -25,6 +25,10 @@ or clone the repository using:
 git clone https://github.com/CountESS-Project/countess-demo/
 ```
 
+This page includes some simple "toy" examples to illustrate the basic
+techniques of developing workflows with CountESS.  For examples of 
+more realistic experiments, see [Further Examples](../further-examples)
+
 ## Example 1: Reading & Counting Sequences
 
 For this simplified example, we'll load up two CSV files with 
@@ -228,7 +232,7 @@ pivot, score and write to CSV steps as before, but duplicated for both DNA and P
 [![Example 2 Image 8](img/example_2_8.png)](img/example_2_8.png)
 [![Example 2 Image 11](img/example_2_11.png)](img/example_2_11.png)
 
-## Example 3: FASTQ and VAMP-seq
+## Example 3: FASTQ
 
 Load this example with `countess_gui example_3.ini`.
 
@@ -271,20 +275,6 @@ on `bin`, giving us columns `count__bin_1`, `count__bin_2`, `count__bin_3` and `
 
 [![Example 3 Image 6](img/example_3_6.png)](img/example_3_6.png)
 
-### VAMP-seq
-
-[VAMP-seq](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5980760/)
-uses a weighted sum of the bins to calculate a score for each variant,
-which is easily implemented in [Python Code](../included-pluyins/#python):
-
-[![Example 3 Image 7](img/example_3_7.png)](img/example_3_7.png)
-
-Files are then written out as before.
-<!--
-[![Example 3 Image 8](img/example_3_8.png)](img/example_3_8.png)
-[![Example 3 Image 9](img/example_3_9.png)](img/example_3_9.png)
--->
-
 ## Example 4: External Metadata
 
 Load this example with `countess_gui example_4.ini`.
@@ -324,3 +314,9 @@ Then we can join the two together using the `filename` column
 in each:
 
 [![Example 4 Image 3](img/example_4_3.png)](img/example_4_3.png)
+
+# Further Examples
+
+This page includes some simple "toy" examples to illustrate the basic
+techniques of developing workflows with CountESS.  For examples of 
+more realistic experiments, see [Further Examples](../further-examples)