diff --git a/README.md b/README.md
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+++ b/README.md
@@ -1,29 +1,59 @@
+# Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers that Drive Differentiation of Pancreatic Cells
 
+This directory contains the scripts for identification of TFs maintaining multipotency of endodermal stem cells during differentiation into pancreatic lineages
+,using TFSEE.
 
-Random Forest of Enhancer Prediction
-http://enhancer.ucsd.edu/renlab/RFECS_enhancer_prediction/
 
+## Dependencies
 
+This code requires python 2.7+ to run.
 
+The pythons scripts require the following python packages:
+- biopython-1.70
+- pandas-0.20.1
+- numpy-1.12.1
+- scikit-learn-0.18.1
+- matplotlib-2.0.2
+- seaborn-0.8.1
+- scipy-0.19.0
 
-# Methods:
 
-1. Call Peaks H3K27ac, H3K4me1 using threshold of 1e-2
-2. Call Peaks H3K4me3 using threshold of 1e-5
-3. Call Transcript units per cell using GRO-seq and GRO-HMM
-4. Merge H3K27ac, H3K4me1, H3K4me3 Peaks within 500bp and make universe filter for at least 1 RPKM in a cell
-5. Merge GRO-seq transcripts and filter for
-    a. +/- 3kb from TSS of protein coding genes Gencode and H3K4me3 pekas
-    b. Merge overlaping transcripts
-    c. Filter for <=9kb Short-Short-Paired and Short-Unpaired
-    d. make universe filter for at least 1 > RPKM SSP and > 2 RPM SUP in a cell
-6. Make Enhancer regions for motif search
-    a. Short-Short-Paired +/- 500 bp center-overlap
-    b. Short-Unpaired +/- bp TSS of transcript
-    c. Histone data +/- bp 500 bp center of mark
-7. De novo motif analyses were performed using the command-line version of MEME (Bailey et al., 2009). The
-following parameters were used for motif prediction: (1) zero or one occurrence per sequence (-
-mod zoops); (2) number of motifs (-nmotifs 15); (3) minimum, maximum width of the motif (-
-minw 8, -maxw 15); and (4) search for motif in given strand and reverse complement strand (-
-revcomp). The predicted motifs from MEME were matched to known motifs using TOMTOM
-(Gupta et al., 2007).
+Install the dependencies.
+
+```sh
+pip install -r requirements.txt
+```
+
+
+#### Pipeline Description
+
+This pipeline uses data from the following analysis to be used as input.
+
+1. De novo identification of enhancers using GRO-seq and [groHMM](http://www.bioconductor.org/packages/release/bioc/html/groHMM.html)
+
+2. Normalize Enhancer Expression using GRO-seq: For each cell line, quantify the GRO-seq reads, RPKM, that fall within a 1 kb region around the center of the overlap for paired enhancer transcripts or from the 5′ end of unpaired enhancer transcripts
+
+3. Normalize Enhancer Expression using ChIP-seq: For each cell line, quantify the ChIP-seq reads, RPKM, from H3K4me1, H3K27ac, and input for each enhancer within the universe of GRO-seq-defined enhancers
+
+4. Motif Predictions: De novo motif analyses on a 1 kb region of expressed enhancers for each cell line using [MEME](http://meme-suite.org/) and  matched to known motifs using TOMTOM and  [JASPAR](http://jaspar.genereg.net/)
+
+5. Normalize Transcription Factor Expression using RNA-seq:  For each cell line, quantify the RNA-seq reads, FPKM, for each  transcription factor that is a binding target for the motifs
+
+6. Calculate TFSEE score to determining cell-type specific enhancer activity, generating:
+* unsupervised hierarchical clustering
+* tSNE representation
+* boxplot representations
+* rank order TF plots
+
+
+### Scripts
+
+- Compute TFSEE to identify cognate transcription factors are under 'analysis'
+ * TFSEE using GRO-seq:
+   * GRO_seq_TFSEE:
+     * matrix_analysis.py: TFSEE score integration
+     * rank_order.py: Rank order TF's clusters
+ * TFSEE using histone modifications ChIP-seq:
+   * GRO_seq_TFSEE:
+     * matrix_analysis.py: TFSEE score integration
+     * rank_order.py: Rank order TF's clusters
diff --git a/ChIP.Rmd b/analysis/ChIP.Rmd
similarity index 100%
rename from ChIP.Rmd
rename to analysis/ChIP.Rmd
diff --git a/E-MTAB-1086.sdrf.txt b/analysis/E-MTAB-1086.sdrf.txt
similarity index 100%
rename from E-MTAB-1086.sdrf.txt
rename to analysis/E-MTAB-1086.sdrf.txt
diff --git a/ES_D0_H3K27ac_filtered_peaks.bed b/analysis/ES_D0_H3K27ac_filtered_peaks.bed
similarity index 100%
rename from ES_D0_H3K27ac_filtered_peaks.bed
rename to analysis/ES_D0_H3K27ac_filtered_peaks.bed
diff --git a/ES_D0_Histone_enhancers.bed b/analysis/ES_D0_Histone_enhancers.bed
similarity index 100%
rename from ES_D0_Histone_enhancers.bed
rename to analysis/ES_D0_Histone_enhancers.bed
diff --git a/ES_D0_Histone_enhancers_1kb.bed b/analysis/ES_D0_Histone_enhancers_1kb.bed
similarity index 100%
rename from ES_D0_Histone_enhancers_1kb.bed
rename to analysis/ES_D0_Histone_enhancers_1kb.bed
diff --git a/ES_D0_gro-seq_enhancers.bed b/analysis/ES_D0_gro-seq_enhancers.bed
similarity index 100%
rename from ES_D0_gro-seq_enhancers.bed
rename to analysis/ES_D0_gro-seq_enhancers.bed
diff --git a/ES_D0_gro-seq_enhancers_1kb.bed b/analysis/ES_D0_gro-seq_enhancers_1kb.bed
similarity index 100%
rename from ES_D0_gro-seq_enhancers_1kb.bed
rename to analysis/ES_D0_gro-seq_enhancers_1kb.bed
diff --git a/ES_D10_H3K27ac_filtered_peaks.bed b/analysis/ES_D10_H3K27ac_filtered_peaks.bed
similarity index 100%
rename from ES_D10_H3K27ac_filtered_peaks.bed
rename to analysis/ES_D10_H3K27ac_filtered_peaks.bed
diff --git a/ES_D10_Histone_enhancers.bed b/analysis/ES_D10_Histone_enhancers.bed
similarity index 100%
rename from ES_D10_Histone_enhancers.bed
rename to analysis/ES_D10_Histone_enhancers.bed
diff --git a/ES_D10_Histone_enhancers_1kb.bed b/analysis/ES_D10_Histone_enhancers_1kb.bed
similarity index 100%
rename from ES_D10_Histone_enhancers_1kb.bed
rename to analysis/ES_D10_Histone_enhancers_1kb.bed
diff --git a/ES_D10_gro-seq_enhancers.bed b/analysis/ES_D10_gro-seq_enhancers.bed
similarity index 100%
rename from ES_D10_gro-seq_enhancers.bed
rename to analysis/ES_D10_gro-seq_enhancers.bed
diff --git a/ES_D10_gro-seq_enhancers_1kb.bed b/analysis/ES_D10_gro-seq_enhancers_1kb.bed
similarity index 100%
rename from ES_D10_gro-seq_enhancers_1kb.bed
rename to analysis/ES_D10_gro-seq_enhancers_1kb.bed
diff --git a/ES_D2_H3K27ac_filtered_peaks.bed b/analysis/ES_D2_H3K27ac_filtered_peaks.bed
similarity index 100%
rename from ES_D2_H3K27ac_filtered_peaks.bed
rename to analysis/ES_D2_H3K27ac_filtered_peaks.bed
diff --git a/ES_D2_Histone_enhancers.bed b/analysis/ES_D2_Histone_enhancers.bed
similarity index 100%
rename from ES_D2_Histone_enhancers.bed
rename to analysis/ES_D2_Histone_enhancers.bed
diff --git a/ES_D2_Histone_enhancers_1kb.bed b/analysis/ES_D2_Histone_enhancers_1kb.bed
similarity index 100%
rename from ES_D2_Histone_enhancers_1kb.bed
rename to analysis/ES_D2_Histone_enhancers_1kb.bed
diff --git a/ES_D2_gro-seq_enhancers.bed b/analysis/ES_D2_gro-seq_enhancers.bed
similarity index 100%
rename from ES_D2_gro-seq_enhancers.bed
rename to analysis/ES_D2_gro-seq_enhancers.bed
diff --git a/ES_D2_gro-seq_enhancers_1kb.bed b/analysis/ES_D2_gro-seq_enhancers_1kb.bed
similarity index 100%
rename from ES_D2_gro-seq_enhancers_1kb.bed
rename to analysis/ES_D2_gro-seq_enhancers_1kb.bed
diff --git a/ES_D5_H3K27ac_filtered_peaks.bed b/analysis/ES_D5_H3K27ac_filtered_peaks.bed
similarity index 100%
rename from ES_D5_H3K27ac_filtered_peaks.bed
rename to analysis/ES_D5_H3K27ac_filtered_peaks.bed
diff --git a/ES_D5_Histone_enhancers.bed b/analysis/ES_D5_Histone_enhancers.bed
similarity index 100%
rename from ES_D5_Histone_enhancers.bed
rename to analysis/ES_D5_Histone_enhancers.bed
diff --git a/ES_D5_Histone_enhancers_1kb.bed b/analysis/ES_D5_Histone_enhancers_1kb.bed
similarity index 100%
rename from ES_D5_Histone_enhancers_1kb.bed
rename to analysis/ES_D5_Histone_enhancers_1kb.bed
diff --git a/ES_D5_gro-seq_enhancers.bed b/analysis/ES_D5_gro-seq_enhancers.bed
similarity index 100%
rename from ES_D5_gro-seq_enhancers.bed
rename to analysis/ES_D5_gro-seq_enhancers.bed
diff --git a/ES_D5_gro-seq_enhancers_1kb.bed b/analysis/ES_D5_gro-seq_enhancers_1kb.bed
similarity index 100%
rename from ES_D5_gro-seq_enhancers_1kb.bed
rename to analysis/ES_D5_gro-seq_enhancers_1kb.bed
diff --git a/ES_D7_H3K27ac_filtered_peaks.bed b/analysis/ES_D7_H3K27ac_filtered_peaks.bed
similarity index 100%
rename from ES_D7_H3K27ac_filtered_peaks.bed
rename to analysis/ES_D7_H3K27ac_filtered_peaks.bed
diff --git a/ES_D7_Histone_enhancers.bed b/analysis/ES_D7_Histone_enhancers.bed
similarity index 100%
rename from ES_D7_Histone_enhancers.bed
rename to analysis/ES_D7_Histone_enhancers.bed
diff --git a/ES_D7_Histone_enhancers_1kb.bed b/analysis/ES_D7_Histone_enhancers_1kb.bed
similarity index 100%
rename from ES_D7_Histone_enhancers_1kb.bed
rename to analysis/ES_D7_Histone_enhancers_1kb.bed
diff --git a/ES_D7_gro-seq_enhancers.bed b/analysis/ES_D7_gro-seq_enhancers.bed
similarity index 100%
rename from ES_D7_gro-seq_enhancers.bed
rename to analysis/ES_D7_gro-seq_enhancers.bed
diff --git a/ES_D7_gro-seq_enhancers_1kb.bed b/analysis/ES_D7_gro-seq_enhancers_1kb.bed
similarity index 100%
rename from ES_D7_gro-seq_enhancers_1kb.bed
rename to analysis/ES_D7_gro-seq_enhancers_1kb.bed
diff --git a/ES_Histone_universe_enhancers.tsv b/analysis/ES_Histone_universe_enhancers.tsv
similarity index 100%
rename from ES_Histone_universe_enhancers.tsv
rename to analysis/ES_Histone_universe_enhancers.tsv
diff --git a/analysis/GRO_seq_TFSEE/.ipynb_checkpoints/Untitled-checkpoint.ipynb b/analysis/GRO_seq_TFSEE/.ipynb_checkpoints/Untitled-checkpoint.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..2fd64429bf421126b7000c94ce0f6fd186fbd01f
--- /dev/null
+++ b/analysis/GRO_seq_TFSEE/.ipynb_checkpoints/Untitled-checkpoint.ipynb
@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/GRO_seq_TFSEE/GRO-seq_enhancers.bed b/analysis/GRO_seq_TFSEE/GRO-seq_enhancers.bed
similarity index 100%
rename from GRO_seq_TFSEE/GRO-seq_enhancers.bed
rename to analysis/GRO_seq_TFSEE/GRO-seq_enhancers.bed
diff --git a/GRO_seq_TFSEE/GRO_filtered_peaks.tsv b/analysis/GRO_seq_TFSEE/GRO_filtered_peaks.tsv
similarity index 100%
rename from GRO_seq_TFSEE/GRO_filtered_peaks.tsv
rename to analysis/GRO_seq_TFSEE/GRO_filtered_peaks.tsv
diff --git a/GRO_seq_TFSEE/H3K27ac_filtered_peaks.bed b/analysis/GRO_seq_TFSEE/H3K27ac_filtered_peaks.bed
similarity index 100%
rename from GRO_seq_TFSEE/H3K27ac_filtered_peaks.bed
rename to analysis/GRO_seq_TFSEE/H3K27ac_filtered_peaks.bed
diff --git a/GRO_seq_TFSEE/H3K27ac_filtered_peaks.tsv b/analysis/GRO_seq_TFSEE/H3K27ac_filtered_peaks.tsv
similarity index 100%
rename from GRO_seq_TFSEE/H3K27ac_filtered_peaks.tsv
rename to analysis/GRO_seq_TFSEE/H3K27ac_filtered_peaks.tsv
diff --git a/GRO_seq_TFSEE/H3K4me1_filtered_peaks.bed b/analysis/GRO_seq_TFSEE/H3K4me1_filtered_peaks.bed
similarity index 100%
rename from GRO_seq_TFSEE/H3K4me1_filtered_peaks.bed
rename to analysis/GRO_seq_TFSEE/H3K4me1_filtered_peaks.bed
diff --git a/GRO_seq_TFSEE/H3K4me1_filtered_peaks.tsv b/analysis/GRO_seq_TFSEE/H3K4me1_filtered_peaks.tsv
similarity index 100%
rename from GRO_seq_TFSEE/H3K4me1_filtered_peaks.tsv
rename to analysis/GRO_seq_TFSEE/H3K4me1_filtered_peaks.tsv
diff --git a/GRO_seq_TFSEE/Input_filtered_peaks.bed b/analysis/GRO_seq_TFSEE/Input_filtered_peaks.bed
similarity index 100%
rename from GRO_seq_TFSEE/Input_filtered_peaks.bed
rename to analysis/GRO_seq_TFSEE/Input_filtered_peaks.bed
diff --git a/GRO_seq_TFSEE/Input_filtered_peaks.tsv b/analysis/GRO_seq_TFSEE/Input_filtered_peaks.tsv
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rename from GRO_seq_TFSEE/Input_filtered_peaks.tsv
rename to analysis/GRO_seq_TFSEE/Input_filtered_peaks.tsv
diff --git a/GRO_seq_TFSEE/SSP_filtered_peaks_sum.tsv b/analysis/GRO_seq_TFSEE/SSP_filtered_peaks_sum.tsv
similarity index 100%
rename from GRO_seq_TFSEE/SSP_filtered_peaks_sum.tsv
rename to analysis/GRO_seq_TFSEE/SSP_filtered_peaks_sum.tsv
diff --git a/GRO_seq_TFSEE/SUNP_filtered_peaks.tsv b/analysis/GRO_seq_TFSEE/SUNP_filtered_peaks.tsv
similarity index 100%
rename from GRO_seq_TFSEE/SUNP_filtered_peaks.tsv
rename to analysis/GRO_seq_TFSEE/SUNP_filtered_peaks.tsv
diff --git a/analysis/GRO_seq_TFSEE/Untitled.ipynb b/analysis/GRO_seq_TFSEE/Untitled.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..c62e98e5d490c09c87519ee193adc622ef6233f2
--- /dev/null
+++ b/analysis/GRO_seq_TFSEE/Untitled.ipynb
@@ -0,0 +1,217 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cluster4 = pd.read_csv('cluster_4_enhancers.csv', index_col=0)\n",
+    "cluster3 = pd.read_csv('cluster_3_enhancers.csv', index_col=0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1371"
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(set(cluster4.index))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1101"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(set(cluster3.index) - set(cluster4.index))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'SSP_236665',\n",
+       " 'SSP_236666',\n",
+       " 'SSP_313311',\n",
+       " 'SUNP_1253075',\n",
+       " 'SUNP_333951',\n",
+       " 'SUNP_415522',\n",
+       " 'SUNP_926025'}"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "set(cluster4.index) - set(cluster3.index)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1364"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "2465-1101"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.4466531440162272"
+      ]
+     },
+     "execution_count": 21,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "1101/2465.0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1371"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(cluster4.index)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1364"
+      ]
+     },
+     "execution_count": 18,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "1371-7"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.9948942377826404"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "1364/1371.0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/GRO_seq_TFSEE/box_plot_cluster_1.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_1.png
similarity index 100%
rename from GRO_seq_TFSEE/box_plot_cluster_1.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_1.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_1_enhancers_rpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_1_enhancers_rpkm.png
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rename from GRO_seq_TFSEE/box_plot_cluster_1_enhancers_rpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_1_enhancers_rpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_1_genes_fpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_1_genes_fpkm.png
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rename from GRO_seq_TFSEE/box_plot_cluster_1_genes_fpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_1_genes_fpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_1_tfs_fpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_1_tfs_fpkm.png
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rename from GRO_seq_TFSEE/box_plot_cluster_1_tfs_fpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_1_tfs_fpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_2.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_2.png
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rename from GRO_seq_TFSEE/box_plot_cluster_2.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_2.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_2_enhancers_rpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_2_enhancers_rpkm.png
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rename from GRO_seq_TFSEE/box_plot_cluster_2_enhancers_rpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_2_enhancers_rpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_2_genes_fpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_2_genes_fpkm.png
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rename from GRO_seq_TFSEE/box_plot_cluster_2_genes_fpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_2_genes_fpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_2_tfs_fpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_2_tfs_fpkm.png
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rename from GRO_seq_TFSEE/box_plot_cluster_2_tfs_fpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_2_tfs_fpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_3.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_3.png
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rename from GRO_seq_TFSEE/box_plot_cluster_3.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_3.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_3_enhancers_rpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_3_enhancers_rpkm.png
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rename from GRO_seq_TFSEE/box_plot_cluster_3_enhancers_rpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_3_enhancers_rpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_3_genes_fpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_3_genes_fpkm.png
similarity index 100%
rename from GRO_seq_TFSEE/box_plot_cluster_3_genes_fpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_3_genes_fpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_3_tfs_fpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_3_tfs_fpkm.png
similarity index 100%
rename from GRO_seq_TFSEE/box_plot_cluster_3_tfs_fpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_3_tfs_fpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_4.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_4.png
similarity index 100%
rename from GRO_seq_TFSEE/box_plot_cluster_4.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_4.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_4_enhancers_rpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_4_enhancers_rpkm.png
similarity index 100%
rename from GRO_seq_TFSEE/box_plot_cluster_4_enhancers_rpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_4_enhancers_rpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_4_genes_fpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_4_genes_fpkm.png
similarity index 100%
rename from GRO_seq_TFSEE/box_plot_cluster_4_genes_fpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_4_genes_fpkm.png
diff --git a/GRO_seq_TFSEE/box_plot_cluster_4_tfs_fpkm.png b/analysis/GRO_seq_TFSEE/box_plot_cluster_4_tfs_fpkm.png
similarity index 100%
rename from GRO_seq_TFSEE/box_plot_cluster_4_tfs_fpkm.png
rename to analysis/GRO_seq_TFSEE/box_plot_cluster_4_tfs_fpkm.png
diff --git a/GRO_seq_TFSEE/closest_genes.py b/analysis/GRO_seq_TFSEE/closest_genes.py
similarity index 100%
rename from GRO_seq_TFSEE/closest_genes.py
rename to analysis/GRO_seq_TFSEE/closest_genes.py
diff --git a/GRO_seq_TFSEE/closest_genes.sh b/analysis/GRO_seq_TFSEE/closest_genes.sh
similarity index 100%
rename from GRO_seq_TFSEE/closest_genes.sh
rename to analysis/GRO_seq_TFSEE/closest_genes.sh
diff --git a/analysis/GRO_seq_TFSEE/cluster1_enriched_tfs.csv b/analysis/GRO_seq_TFSEE/cluster1_enriched_tfs.csv
new file mode 100644
index 0000000000000000000000000000000000000000..4eb49fc4504b7b48e732445dce2502a115f112e2
--- /dev/null
+++ b/analysis/GRO_seq_TFSEE/cluster1_enriched_tfs.csv
@@ -0,0 +1,65 @@
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diff --git a/GRO_seq_TFSEE/cluster1_enriched_tfs.png b/analysis/GRO_seq_TFSEE/cluster1_enriched_tfs.png
similarity index 100%
rename from GRO_seq_TFSEE/cluster1_enriched_tfs.png
rename to analysis/GRO_seq_TFSEE/cluster1_enriched_tfs.png
diff --git a/analysis/GRO_seq_TFSEE/cluster2_enriched_tfs.csv b/analysis/GRO_seq_TFSEE/cluster2_enriched_tfs.csv
new file mode 100644
index 0000000000000000000000000000000000000000..b9f8c368e948ecccc37fc682ca94b9b0ccc01a5c
--- /dev/null
+++ b/analysis/GRO_seq_TFSEE/cluster2_enriched_tfs.csv
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diff --git a/GRO_seq_TFSEE/cluster2_enriched_tfs.png b/analysis/GRO_seq_TFSEE/cluster2_enriched_tfs.png
similarity index 100%
rename from GRO_seq_TFSEE/cluster2_enriched_tfs.png
rename to analysis/GRO_seq_TFSEE/cluster2_enriched_tfs.png
diff --git a/analysis/GRO_seq_TFSEE/cluster3_enriched_tfs.csv b/analysis/GRO_seq_TFSEE/cluster3_enriched_tfs.csv
new file mode 100644
index 0000000000000000000000000000000000000000..21e5d04eee0c0158dcc85551c7b69ee028729de7
--- /dev/null
+++ b/analysis/GRO_seq_TFSEE/cluster3_enriched_tfs.csv
@@ -0,0 +1,35 @@
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diff --git a/GRO_seq_TFSEE/cluster3_enriched_tfs.png b/analysis/GRO_seq_TFSEE/cluster3_enriched_tfs.png
similarity index 100%
rename from GRO_seq_TFSEE/cluster3_enriched_tfs.png
rename to analysis/GRO_seq_TFSEE/cluster3_enriched_tfs.png
diff --git a/analysis/GRO_seq_TFSEE/cluster4_enriched_tfs.csv b/analysis/GRO_seq_TFSEE/cluster4_enriched_tfs.csv
new file mode 100644
index 0000000000000000000000000000000000000000..0d5916ff99c5d6ed46a1ffbe1829bb11a058ce5e
--- /dev/null
+++ b/analysis/GRO_seq_TFSEE/cluster4_enriched_tfs.csv
@@ -0,0 +1,35 @@
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diff --git a/GRO_seq_TFSEE/cluster4_enriched_tfs.png b/analysis/GRO_seq_TFSEE/cluster4_enriched_tfs.png
similarity index 100%
rename from GRO_seq_TFSEE/cluster4_enriched_tfs.png
rename to analysis/GRO_seq_TFSEE/cluster4_enriched_tfs.png
diff --git a/GRO_seq_TFSEE/cluster_1_enhancers.csv b/analysis/GRO_seq_TFSEE/cluster_1_enhancers.csv
similarity index 100%
rename from GRO_seq_TFSEE/cluster_1_enhancers.csv
rename to analysis/GRO_seq_TFSEE/cluster_1_enhancers.csv
diff --git a/GRO_seq_TFSEE/cluster_1_enhancers_locations.bed b/analysis/GRO_seq_TFSEE/cluster_1_enhancers_locations.bed
similarity index 100%
rename from GRO_seq_TFSEE/cluster_1_enhancers_locations.bed
rename to analysis/GRO_seq_TFSEE/cluster_1_enhancers_locations.bed
diff --git a/GRO_seq_TFSEE/cluster_1_genes.txt b/analysis/GRO_seq_TFSEE/cluster_1_genes.txt
similarity index 100%
rename from GRO_seq_TFSEE/cluster_1_genes.txt
rename to analysis/GRO_seq_TFSEE/cluster_1_genes.txt
diff --git a/GRO_seq_TFSEE/cluster_1_tfs.csv b/analysis/GRO_seq_TFSEE/cluster_1_tfs.csv
similarity index 100%
rename from GRO_seq_TFSEE/cluster_1_tfs.csv
rename to analysis/GRO_seq_TFSEE/cluster_1_tfs.csv
diff --git a/GRO_seq_TFSEE/cluster_2_enhancers.csv b/analysis/GRO_seq_TFSEE/cluster_2_enhancers.csv
similarity index 100%
rename from GRO_seq_TFSEE/cluster_2_enhancers.csv
rename to analysis/GRO_seq_TFSEE/cluster_2_enhancers.csv
diff --git a/GRO_seq_TFSEE/cluster_2_enhancers_locations.bed b/analysis/GRO_seq_TFSEE/cluster_2_enhancers_locations.bed
similarity index 100%
rename from GRO_seq_TFSEE/cluster_2_enhancers_locations.bed
rename to analysis/GRO_seq_TFSEE/cluster_2_enhancers_locations.bed
diff --git a/GRO_seq_TFSEE/cluster_2_genes.txt b/analysis/GRO_seq_TFSEE/cluster_2_genes.txt
similarity index 100%
rename from GRO_seq_TFSEE/cluster_2_genes.txt
rename to analysis/GRO_seq_TFSEE/cluster_2_genes.txt
diff --git a/GRO_seq_TFSEE/cluster_2_tfs.csv b/analysis/GRO_seq_TFSEE/cluster_2_tfs.csv
similarity index 100%
rename from GRO_seq_TFSEE/cluster_2_tfs.csv
rename to analysis/GRO_seq_TFSEE/cluster_2_tfs.csv
diff --git a/GRO_seq_TFSEE/cluster_3_enhancers.csv b/analysis/GRO_seq_TFSEE/cluster_3_enhancers.csv
similarity index 100%
rename from GRO_seq_TFSEE/cluster_3_enhancers.csv
rename to analysis/GRO_seq_TFSEE/cluster_3_enhancers.csv
diff --git a/GRO_seq_TFSEE/cluster_3_enhancers_locations.bed b/analysis/GRO_seq_TFSEE/cluster_3_enhancers_locations.bed
similarity index 100%
rename from GRO_seq_TFSEE/cluster_3_enhancers_locations.bed
rename to analysis/GRO_seq_TFSEE/cluster_3_enhancers_locations.bed
diff --git a/GRO_seq_TFSEE/cluster_3_genes.txt b/analysis/GRO_seq_TFSEE/cluster_3_genes.txt
similarity index 100%
rename from GRO_seq_TFSEE/cluster_3_genes.txt
rename to analysis/GRO_seq_TFSEE/cluster_3_genes.txt
diff --git a/GRO_seq_TFSEE/cluster_3_tfs.csv b/analysis/GRO_seq_TFSEE/cluster_3_tfs.csv
similarity index 100%
rename from GRO_seq_TFSEE/cluster_3_tfs.csv
rename to analysis/GRO_seq_TFSEE/cluster_3_tfs.csv
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diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..492decf2082a83c62f44268fac8ba42e564bb0c2
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,7 @@
+biopython==1.70
+pandas==0.20.1
+numpy==1.12.1
+scikit-learn==0.18.1
+matplotlib==2.0.2
+seaborn==0.8.1
+scipy==0.19.0