Update README.md

README.md

@@ -45,6 +45,8 @@ In general, you need to make three objects (Train, TopModel and Analysis).
 
 The Train object can be initialized either from (a) single cell RNA-seq dataset or (b) single cell ATAC-seq or (c) bulk RNA-seq.
 
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 Training part can be time-consuming depending on how big your data is, however you can learn each train model per random state in different jobs and then combine all together. Look at [this tutorial](tutorials/make_train_object.ipynb) for mor information.
 
 For guidance on using Topyfic to analyze your data look at our more depth-in tutorials:
@@ -53,8 +55,15 @@ For guidance on using Topyfic to analyze your data look at our more depth-in tut
 - [Analysing single cell microglia data](tutorials/microglia_all_genes/microglia.ipynb): Analysing single cell microglia data from [Model-AD portal](https://www.model-ad.org/).
 - [Analysing ENCODE time course hippocampus data](tutorials/ENCODE_Hipp_parse_10x/analysing.ipynb): Analysing parse single-nucleus RNA-seq data and RNA part of 10x multiome hippocampus data from ENCODE.
 
+If you are using other methods to learn your topics, but you are still interested in doing downstream analysis, you can embeded your results in the format describe [here](tutorials/topic_modeling_model.md). Once you have all your files ready you can embed them Topyfic format following the instruction in the same [tutorial](tutorials/topic_modeling_model.md).
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+### Snakemake workflow
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+The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
+
+To focus more deeply on downstream analyses, I provide a Snakemake workflow to train and build three necessary objects (Train, TopModel, and Analysis).
 
-If you are using other methods to learn your topics but you are still interested in doing downstream analysis, you can embeded your results in the format describe [here](tutorials/topic_modeling_model.md). Once you have all your files ready you can embed them Topyfic format following the instruction in the same [tutorial](tutorials/topic_modeling_model.md).
+For more information on how to run Topyfic Snakemake, please look [here](workflow/snakemake).
 
 ## Cite