split up documentation (#74)

Author: mccalluc

COMMANDS.md

@@ -1,6 +1,8 @@
 ### Converting tsv files to mrmatrix
 
+```
 python scripts/tsv-to-mrmatrix.py data/dense.tsv data/dense.mrmatrix
+```
 
 ### Calculating gene coverage
 

README.md

@@ -1,6 +1,11 @@
 # Clodius <img src="https://travis-ci.org/hms-dbmi/clodius.svg?branch=develop"/>
 
-## Quick start without docker
+Displaying large amounts of data often requires first turning it into
+not-so-large amounts of data. Clodius is a program and library designed
+to aggregate large datasets to make them easy to display at different
+resolutions.
+
+## Demo
 
 Install the clodius package:
 
@@ -18,6 +23,21 @@ The output files can then be displayed using the [higlass-docker container](http
 
 [More examples](COMMANDS.md) are available.
 
+## File Types
+
+- Non-genomic Rasters
+  - [TSV Files](docs/raster/tsv.rst)
+- Genomic Data
+  - [Bed Files](docs/genomic/bed.rst)
+  - [BedGraph Files](docs/genomic/bedgraph.rst)
+  - [Bedpe-like Files](docs/genomic/bedpe.rst)
+  - [BigWig Files](docs/genomic/bigwig.rst)
+  - [Chromosome Sizes](docs/genomic/chromosome-sizes.rst)
+  - [Cooler Files](docs/genomic/cooler.rst)
+  - [Gene Annotation](docs/genomic/gene-annotation.rst)
+  - [HiTile Files](docs/genomic/hitile.rst)
+  - [Multivec Files](docs/genomic/multivec.rst)
+
 ## Development