Small changes according to issue 235 and reordering of the installati…

…on section (#236)

Co-authored-by: Yotam Constantini <[email protected]>

README.md

@@ -72,7 +72,7 @@ Klopfenstein DV, Zhang L, Pedersen BS, ... Tang H [GOATOOLS: A Python library fo
 _Scientific reports_ | (2018) 8:10872 | DOI:10.1038/s41598-018-28948-z
 
 - **GO Grouping**:
- Visualize the major findings in a gene ontology enrichment analysis (GEOA) more easily with grouping.
+ Visualize the major findings in a gene ontology enrichment analysis (GOEA) more easily with grouping.
  A detailed description of GOATOOLS GO grouping is found in the
  [manuscript](https://www.nature.com/articles/s41598-018-28948-z).
 - **Compare GO lists**:
@@ -88,46 +88,52 @@ _Scientific reports_ | (2018) 8:10872 | DOI:10.1038/s41598-018-28948-z
 
 ## Installation
 
-Make sure your Python version >= 3.7, install the latest stable
-version via PyPI:
+Make sure your Python version >= 3.7, and download an
+`.obo` file of the most current
+[GO](http:https://geneontology.org/docs/download-ontology):
 
 ```bash
-pip install goatools
+wget http:https://current.geneontology.org/ontology/go-basic.obo
 ```
 
-To install the development version:
+or `.obo` file for the most current [GO
+Slim](http:https://geneontology.org/docs/go-subset-guide/) terms (e.g.
+generic GOslim) :
 
 ```bash
-pip install git+git:https://github.com/tanghaibao/goatools.git
+wget http:https://current.geneontology.org/ontology/subsets/goslim_generic.obo
 ```
 
-`.obo` file for the most current
-[GO](http:https://geneontology.org/page/download-ontology):
+
+
+### [PyPI](https://pypi.org/project/goatools/)
 
 ```bash
-wget http:https://geneontology.org/ontology/go-basic.obo
+pip install goatools
 ```
 
-`.obo` file for the most current [GO
-Slim](http:https://geneontology.org/page/go-slim-and-subset-guide) terms (e.g.
-generic GOslim) :
+To install the development version:
+
+```bash
+pip install git+git:https://github.com/tanghaibao/goatools.git
+```
 
+### [Bioconda](http:https://bioconda.github.io/recipes/goatools/README.html?highlight=goatools)
 ```bash
-wget http:https://www.geneontology.org/ontology/subsets/goslim_generic.obo
+conda install -c bioconda goatools
 ```
 
 ## Dependencies
 
-- Simplest is to install via pip as above or
- [bioconda](http:https://bioconda.github.io/recipes/goatools/README.html?highlight=goatools).
+When installing via PyPI or Bioconda as described above, all dependencies are automatically downloaded.
+Alternatively, you can manually install:
 
 - For statistical testing of GO enrichment:
-
  - [`scipy.stats.fisher_exact`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html)
  - `statsmodels` (optional) for access to a variety of statistical tests for GOEA
 
-- To plot the ontology lineage, install one of these two options:
 
+- To plot the ontology lineage, install one of these two options:
  - [Graphviz](http:https://www.graphviz.org/), for graph visualization.
  - [pygraphviz](http:https://networkx.lanl.gov/pygraphviz/), Python binding for communicating with Graphviz:
  - [pydot](https://code.google.com/p/pydot/), a Python interface to Graphviz's Dot language.
@@ -282,8 +288,8 @@ strategy which may lead to slightly different q-values between runs.
 
 ### Run a Ontology Enrichment Analysis (GOEA)
 
-[goea_nbt3102](notebooks/goea_nbt3102.ipynb) 
-[human phenotype ontologies](notebooks/Enrichment_analyses_human_phenotype_ontology.ipynb) 
+[goea_nbt3102](notebooks/goea_nbt3102.ipynb)
+[human phenotype ontologies](notebooks/Enrichment_analyses_human_phenotype_ontology.ipynb)
 
 ### Show many study genes are associated with RNA, translation, mitochondria, and ribosomal