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LBMC
RMI2
TDD_project
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850aeba1
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850aeba1
authored
1 year ago
by
dcluet
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Add explanation on transcript selection
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850aeba1
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@@ -99,7 +99,21 @@ The final arborescence should be:
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@@ -99,7 +99,21 @@ The final arborescence should be:
*
filtred_genes_Lympho_Resting.csv
*
filtred_genes_Lympho_Resting.csv
*
filtred_genes_Lympho_Activated.csv
*
filtred_genes_Lympho_Activated.csv
*
DESeqresults_lympho_activation_untreated.csv
*
DESeqresults_lympho_activation_untreated.csv
> The `filtred_genes_Lympho_Resting.csv` and
> `filtred_genes_Lympho_Activated.csv` files
> are used to focus the machine learning process on pre-selected transcripts.
>
> This selection was based on the gene normalized read counts of the 3h
> Triptolide libraries (~5000 genes in Resting and ~6000 genes in Activated
> T-cells). Of these, only genes with completed observations in all biological
> replicates (including ribosome profiling libraries) and for all
> transcript features used to build the model, as well as at least 15% of
> observed degradation at 3h, were kept for further analysis.
>
> The `DESeqresults_lympho_activation_untreated.csv` file is used to add the
> `log2FoldChange` to the database.
> This column is used as parameter for the `deltaTDD` and `deltaTID` scores.
## Generate a Random Forest model
## Generate a Random Forest model
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