Start NCBI Gene example

doc/md/README_NCBI_gene.md

@@ -0,0 +1,30 @@
+# NCBI GeneID and Symbol
+Example of printing gene symbols (instead of geneids) from NCBI gene in a GOEA results table.
+
+1. Download NCBI gene information into gene_result.txt
+2. Convert gene_result.txt file into Python 
+3. Create a geneid2symbol.txt ASCII file
+4. Run GOEA using --id2name flag
+
+## Download NCBI gene information into gene_result.txt
+ * Go to NCBI Gene in your browser https://www.ncbi.nlm.nih.gov/gene/
+ * Type a search pattern and hit the "Search" button.    
+   For example, to download all human protein-coding genes:
+```
+genetype protein coding[Properties] AND "9606"[Taxonomy ID] AND alive[property] 
+```
+
+    | NCBI Search text                    | Description
+    |-------------------------------------|----------------------
+    | genetype protein coding[Properties] | Protein-coding genes
+    | "9606"[Taxonomy ID]                 | human
+    | alive[property]                     | NOT obsolete
+
+![NCBI Gene Search](doc/images/NCBI_gene_search.png)
+
+## Convert gene_result.txt file into Python 
+## Create a geneid2symbol.txt ASCII file
+## Run GOEA using --id2name flag
+
+
+Copyright (C) 2016-2018, DV Klopfenstein, Haibao Tang et al. All rights reserved.

doc/md/README_find_enrichment.md

@@ -1,16 +1,17 @@
-# Examples of Gene Ontolog Enrichment Analyses (GOEA) from the command-line
+# Gene Ontolog Enrichment Analyses (GOEA) from the command-line
+
+## Run GOEA and print GO terms
 
-**Run GOEA and print GO terms**:
   1. [with **uncorrected pvalues < 0.05** to the screen](#1-print-go-terms-with-uncorrected-pvalues--005-to-the-screen-default):
     (default)
   2. [with **uncorrected pvalues < 0.05** to the screen, **grouped**](#2-print-go-terms-with-uncorrected-pvalues--005-to-the-screen-grouped): **--sections=...**
   3. [with **uncorrected pvalues < 0.05** to files](#3-print-go-terms-with-uncorrected-pvalues--005-to-an-xlsx-file):
     **--outfile=goea.xlsx**
   4. [with **Benjamini-Hochberg pvalues < 0.05** (plus bonferroni, sidak, holm)](#4-print-go-terms-with-benjamini-hochberg-pvalues--005) 
     **--pval_field=fdr_bh**    
-  5. [with **Benjamini-Hochberg (only) pvalues < 0.05** to an **xlsx** file](#5-print-go-terms-with-benjamini-hochberg-only-pvalues--005-to-an-xlsx-file)     
+  5. [with **Benjamini-Hochberg pvalues < 0.05** to an **xlsx** file](#5-print-go-terms-with-benjamini-hochberg-only-pvalues--005-to-an-xlsx-file)     
     **--method=fdr_bh --outfile=goea_fdr_bh_flat.xlsx**    
-  6. [with **Benjamini-Hochberg (only) pvalues < 0.05** to an **xlsx** file, **grouped**](#6-print-go-terms-with-benjamini-hochberg-only-pvalues--005-to-an-xlsx-file-grouped)     
+  6. [with **Benjamini-Hochberg pvalues < 0.05** to an **xlsx** file, **grouped**](#6-print-go-terms-with-benjamini-hochberg-only-pvalues--005-to-an-xlsx-file-grouped)     
     **--method=fdr_bh --outfile=goea_fdr_bh_grpd.xlsx --sections...**    
   7. [regardless of pvalue **(ALL GO terms)**](#7-print-all-go-terms-regardless-of-pvalue)
     **--pval=-1**