minor changes, add more version info to README

06_preprocess_retina.ipynb

@@ -295,8 +295,8 @@
     "\n",
     "#use batch/replicate identity to get the two larger batches\n",
     "assert np.all(replicate_names==np.array(['Bipolar1','Bipolar2','Bipolar3','Bipolar4','Bipolar5','Bipolar6']))\n",
-    "shekhar_replicate_ids = np.array([1, 2, 3, 4, 1, 2]) #see suppl. text of macosko paper\n",
-    "shekhar_batch_ids = np.array([1, 1, 1, 1, 2, 2]) #see suppl. text of macosko paper\n",
+    "shekhar_replicate_ids = np.array([1, 2, 3, 4, 1, 2]) \n",
+    "shekhar_batch_ids = np.array([1, 1, 1, 1, 2, 2]) \n",
     "batches = shekhar_batch_ids[replicates]"
    ]
   },

README.md

@@ -30,6 +30,14 @@ For questions or feedback, feel free to use the issue system or email us.
 ### Pre-requisites
 
 - Python (version used in the paper: `3.6.9`)
+- `numpy` (version used in this paper `1.18.1`)
+- `pandas` (version used in this paper `1.0.1`)
+- `scipy` (version used in this paper `1.4.1`)
+- `seaborn` (version used in this paper `0.10.0`)
+- `matplotlib` (version used in this paper `3.1.3`)
+- `statsmodels` (version used in this paper `0.11.1`)
+- `sklearn` (version used in this paper `0.22.1`)
+- `anndata` from https://anndata.readthedocs.io (version used in this paper `0.7.1`)
 - `FIt-SNE` by George C. Linderman from https://github.com/KlugerLab/FIt-SNE (version used in the paper: `1.2.1`, https://github.com/KlugerLab/FIt-SNE/releases/tag/v1.2.1)
 - `FFTW` from http://www.fftw.org (version used in the paper: `3.3.8`)
 - `rpy2` from https://rpy2.github.io/ (version used in the paper `3.2.6`, along with R version `3.6.2`)