DOC: Add make help usage and simplify GitHub repository name

README.md

@@ -51,20 +51,38 @@ where each well corresponds to a protein being knocked down.
 Usage
 -----
 
+All programs are run using a single `Makefile`.
+Type the `make help` to see a list of options:
+
+``` sh
+Usage: make [TARGET] ...
+
+Targets:
+all                (Default) Run full pipeline from image processing to plots.
+help               Show this help.
+z-projection       Generate maximum intensity projection images.
+cellprofiler       Collect statistics about all images.
+gui-cellprofiler   Interactively run CellProfiler.
+stats              Find significant wells from cellprofiler measurements.
+clean-all          Delete all output.
+```
+
 Run the `Makefile` in this directory to generate all results.
 
 ``` sh
-make
+make all
 ```
 
+Depending
+
 To tune CellProfiler's image processing,
 it is helpful to save results in a separate directory.
 One can clone this repository using a different directory name,
 and link to the processed image set of the original:
 
 ``` sh
 cd ..
-git clone git@github.uconn.edu:MelloneLab/RNAi_plate_analysis_all.git rnai-screen-tf_20170314
+git clone git@github.uconn.edu:MelloneLab/rnai-screen-tf.git rnai-screen-tf_20170314
 cd rnai-screen-tf_20170314
 rm -rf z_projection
 ln -s ../../rnai-screen-tf/results/z_projection z_projection