diff --git a/.gitignore b/.gitignore
index e1c59fb..422e5e6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -50,4 +50,25 @@ zebrafish/.ipynb_checkpoints/
 zebrafish/cache/
 zebrafish/data/
 zebrafish/figures/
-zebrafish/write/
\ No newline at end of file
+zebrafish/write/
+comparisons/paul15_monocle2/data/
+comparisons/paul15_monocle2/figures/
+comparisons/simulated_data/README.md
+comparisons/simulated_data/data/
+comparisons/simulated_data/eclair/ECLAIR_instance/
+comparisons/simulated_data/eclair/X_krumsiek11.txt
+comparisons/simulated_data/eclair/X_krumsiek11_blobs.txt
+comparisons/simulated_data/eclair/X_krumsiek11_scaled.txt
+comparisons/simulated_data/eclair/eclair_plots.ipynb
+comparisons/simulated_data/eclair/figures/
+comparisons/simulated_data/figures/
+comparisons/simulated_data/stemID/RaceID3_StemID2_class.R
+comparisons/simulated_data/stemID/RaceID3_StemID2_sample.R
+comparisons/simulated_data/stemID/Rplots_X_krumsiek11_blobs_shifted_1.png
+comparisons/simulated_data/stemID/Rplots_X_krumsiek11_blobs_shifted_2.png
+comparisons/simulated_data/stemID/X_krumsiek11_blobs_shifted.csv
+comparisons/simulated_data/stemID/X_krumsiek11_shifted.csv
+comparisons/simulated_data/write/
+deep_learning/data/
+deep_learning/figures/
+deep_learning/write/
\ No newline at end of file