--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/commands_examples	Thu Sep 24 02:17:05 2020 +0000
@@ -0,0 +1,78 @@
+#Commands to reproduce use-case examples
+
+
+#### Use-case 1a #####
+
+$ cd <path>/SimText
+
+$ Rscript pubmed_by_queries.R \
+ --input examples/data/1a/clingen_data \
+ --output examples/data/1a/pubmed_by_queries_output \
+ --number 500 \
+ --abstract \
+ --install_packages
+
+$ Rscript text_to_wordmatrix.R \
+ --input "examples/data/1a/pubmed_by_queries_output" \
+ --output "examples/data/1a/clingen_data_matrix" \
+ --number 100 \
+ --install_packages
+
+$ Rscript simtext_app.R \
+ --input "examples/data/1a/clingen_data" \
+ --matrix "examples/data/1a/clingen_data_matrix" \
+ --install_packages
+
+
+
+#### Use-case 1b #####
+
+$ cd <path>/SimText
+
+$ Rscript pubmed_by_queries.R \
+ --input "examples/data/1b/clingen_data" \
+ --output "examples/data/1b/pubmed_by_queries_output" \
+ --number 500 \
+ --install_packages
+
+$ Rscript pmids_to_pubtator_matrix.R \
+ --input "examples/data/1b/pubmed_by_queries_output"  \
+ --output "examples/data/1b/clingen_data_matrix" \
+ --categories Disease Gene \
+ --number 100 \
+ --install_packages
+
+$ Rscript simtext_app.R \
+ --input "examples/data/1b/clingen_data" \
+ --matrix "examples/data/1b/clingen_data_matrix" \
+ --install_packages
+
+
+#### Use-case 2 #####
+
+cd <path>/SimText
+
+$ Rscript abstracts_by_pmids.R \
+ --input "examples/data/2/researcher_data.txt" \
+ --output "examples/data/2/abstracts_by_pmids_output"
+
+$ Rscript text_to_wordmatrix.R \
+ --input "examples/data/2/abstracts_by_pmids_output" \
+ --output "examples/data/2/researcher_data_matrix" \
+ --number 50
+
+$ Rscript simtext_app.R \
+ --input "examples/data/2/researcher_data.txt" \
+ --matrix "examples/data/2/researcher_data_matrix"
+
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