Commit db46b58a authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

Merge branch 'doc/fix' into 'dev'

doc/vidjil-format.md: fix backquotes

See merge request !924
parents 88706dd8 c5ef6cce
Pipeline #224974 passed with stages
in 82 minutes and 51 seconds
......@@ -11,6 +11,7 @@ build_doc:
paths:
- site/
expire_in: 1 month
when: always
only:
- /^[^\/]*doc[^\/]*\//
# branch name should contain doc before the first /
......
......@@ -529,7 +529,7 @@ file in JSON format must be created, as in the following example:
]
}
}
````
```
and given to `vidjil-algo` by means of the flag `--label-json
spikes.json`. Notice that the family of each spike-in must be
......@@ -543,7 +543,7 @@ one to the `Fuse command:` field in the analysis config:
```javascript
-t 100 --pre spike_normalization.py
````
```
The `spike-normalization.py` script is responsible for collecting read
counts for the spike-ins, combining them with their copy numbers, and
......@@ -583,7 +583,7 @@ data fields in the `vidjil` file. Part of the info is set into an
"IGK"
]
}
````
```
The item `coefficients`, one per family, contains the coefficients that
multiplied by a read count will yield a normalized value. Here, `UNI`
......@@ -613,7 +613,7 @@ and are arrays containing one value per time point.
"normalized_reads": [ 195.50763372699805 ]
}
]
````
```
Here, field `R2` indicates the Pearson R2 coefficient for the linear
regression used in this clone; `copy_number` is the estimated copy
......
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