update notebook link to github file

README.md

@@ -4,7 +4,7 @@
 Palantir
 ------
 
-Palantir is an algorithm to align cells along differentiation trajectories. Palantir models differentiation as a stochastic process where stem cells differentiate to terminally differentiated cells by a series of steps through a low dimensional phenotypic manifold. Palantir effectively captures the continuity in cell states and the stochasticity in cell fate determination. Palantir has been designed to work with multidimensional single cell data from diverse technologies such as Mass cytometry and single cell RNA-seq. 
+Palantir is an algorithm to align cells along differentiation trajectories. Palantir models differentiation as a stochastic process where stem cells differentiate to terminally differentiated cells by a series of steps through a low dimensional phenotypic manifold. Palantir effectively captures the continuity in cell states and the stochasticity in cell fate determination. Palantir has been designed to work with multidimensional single cell data from diverse technologies such as Mass cytometry and single cell RNA-seq.
 
 
 ## Installation and dependencies
@@ -29,7 +29,8 @@ here: https://palantir.readthedocs.io
 - [Replicate 2 (Rep2)](https://s3.amazonaws.com/dp-lab-data-public/palantir/human_cd34_bm_rep2.h5ad)
 - [Replicate 3 (Rep3)](https://s3.amazonaws.com/dp-lab-data-public/palantir/human_cd34_bm_rep3.h5ad)
 
-This notebook details how to use the data in `Python` and `R`: http://nbviewer.jupyter.org/github/dpeerlab/Palantir/blob/master/notebooks/manuscript_data.ipynb
+This notebook details how to use the data in `Python` and `R`:
+https://github.com/dpeerlab/Palantir/blob/master/notebooks/manuscript_data.ipynb
 
 ## Comparison to trajectory detection algorithms
 Notebooks detailing the generation of results comparing Palantir to trajectory detection algorithms are available [here](https://github.com/dpeerlab/Palantir/blob/master/notebooks/comparisons)
@@ -107,20 +108,20 @@ Release Notes
 
 
 ### Version 1.1.0
- * Replaced rpy2 with pyGAM for computing gene expression trends. 
- * Updated tutorial and plotting functions 
+ * Replaced rpy2 with pyGAM for computing gene expression trends.
+ * Updated tutorial and plotting functions
 
 
 ### Version 1.0.0
 
- * A fix to [issue#41](https://github.com/dpeerlab/Palantir/issues/41) 
+ * A fix to [issue#41](https://github.com/dpeerlab/Palantir/issues/41)
  * A fix to [issue#42](https://github.com/dpeerlab/Palantir/issues/42)
  * Revamped tutorial with support for Anndata and force directed layouts
 
 ### Version 0.2.6
 
  * A fix to [issue#33](https://github.com/dpeerlab/Palantir/issues/33) and [issue#31](https://github.com/dpeerlab/Palantir/issues/31)
- 
+
 ### Version 0.2.5
 
  * A fix related to [issue#28](https://github.com/dpeerlab/Palantir/issues/28). When identifying terminal states, duplicate values were generated instead of unique ones.