Add training notebook

songlab-cal · Oct 11, 2023 · 0837899 · 0837899
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diff --git a/README.md b/README.md
@@ -76,11 +76,12 @@ python -m gpn.ss.run_vep variants.parquet genome.fa.gz 512 your_output_dir resul
 ### Examples
 * Play with the model: `examples/msa/basic_example.ipynb`
 * Variant effect prediction: `examples/msa/vep.ipynb`
+* Training (human): `examples/msa/training.ipynb`
 
 ### Code and resources from specific papers
 * [Human](analysis/human)
 
-### Training on your own data
+### Training on other species (e.g. plants)
 Under construction.
 
 ## Citation

diff --git a/analysis/human/README.md b/analysis/human/README.md
@@ -8,5 +8,5 @@
 * [Logo track at UCSC Genome Browser](https://genome.ucsc.edu/s/gbenegas/gpn-msa-sapiens)
 
 ## Reproducing the analysis
-* Dependencies: `envs/general.yaml`
+* Dependencies: `workflow/envs/general.yaml`
 * Running Snakemake: `snakemake --cores all`
diff --git a/examples/msa/basic_example.ipynb b/examples/msa/basic_example.ipynb
@@ -7,7 +7,7 @@
     "user_expressions": []
    },
    "source": [
-    "# Basic example with GPN-MSA"
+    "# GPN-MSA: basic example"
    ]
   },
   {