Update README with tip for installing with pipenv

Also satiate my markdown linter.

Author: JonathanShor

README.md

@@ -1,22 +1,30 @@
 # DoubletDetection
+
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2678042.svg)](https://doi.org/10.5281/zenodo.2678042)
 [![Documentation Status](https://readthedocs.org/projects/doubletdetection/badge/?version=latest)](https://doubletdetection.readthedocs.io/en/latest/?badge=latest)
 
-
 DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell RNA-seq count matrices.
 
+## Installing DoubletDetection
 
-To install DoubletDetection:
-
-```
+```bash
 git clone https://github.com/JonathanShor/DoubletDetection.git
 cd DoubletDetection
 pip3 install .
 ```
 
-To run basic doublet classification:
+If you are using `pipenv` as your virtual environment, it may struggle installing from the setup.py due to our custom Phenograph requirement.
+If so, try the following in the cloned repo:
 
+```bash
+pipenv run pip3 install .
 ```
+
+## Running DoubletDetection
+
+To run basic doublet classification:
+
+```Python
 import doubletdetection
 clf = doubletdetection.BoostClassifier()
 # raw_counts is a cells by genes count matrix
@@ -27,6 +35,7 @@ labels = clf.fit(raw_counts).predict()
 - `labels` is a 1-dimensional numpy ndarray with the value 1 representing a detected doublet, 0 a singlet, and `np.nan` an ambiguous cell.
 
 The classifier works best when
+
 - There are several cell types present in the data
 - It is applied individually to each run in an aggregated count matrix
 
@@ -35,10 +44,11 @@ In `v2.5` we have added a new experimental clustering method (`scanpy`'s Louvain
 See our [jupyter notebook](https://nbviewer.jupyter.org/github/JonathanShor/DoubletDetection/blob/master/tests/notebooks/PBMC_8k_vignette.ipynb) for an example on 8k PBMCs from 10x.
 
 ## Obtaining data
-Data can be downloaded from the [10x website](https://support.10xgenomics.com/single-cell/datasets).
 
+Data can be downloaded from the [10x website](https://support.10xgenomics.com/single-cell/datasets).
 
 ## Citations
+
 bioRxiv submission and journal publication expected in the coming months. Please use the following for now:
 
 Gayoso, Adam, & Shor, Jonathan. (2018, July 17). DoubletDetection (Version v2.4). Zenodo. http://doi.org/10.5281/zenodo.2678042