Merge master

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rliger2
 Version: 1.99.0
-Date: 2023-11-02
+Date: 2023-11-09
 Type: Package
 Title: Linked Inference of Genomic Experimental Relationships
 Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

NEWS.md

@@ -12,11 +12,12 @@
 Now named by `runINMF()`, `runUINMF()` and `runOnlineINMF()` respectively, and wrapped in 
 `runIntegration()`.
 
-## rliger 1.0.1
+## rliger2 1.0.1
 
 - Allow setting mito pattern in `getMitoProportion()` #271
 - Fix efficiency issue when taking the log of norm.data (e.g. `runWilcoxon`)
 - Add runable examples to all exported functions when possible
 - Fix typo in online_iNMF matrix initialization
+- Adapt to Seurat5
 - Other minor fixes
 

README.md

@@ -8,8 +8,8 @@
 
 LIGER (installed as `rliger` ) is a package for integrating and analyzing multiple single-cell datasets, developed by the Macosko lab and maintained/extended by the Welch lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.
 
-Check out our [Cell paper](https://doi.org/10.1016/j.cell.2019.05.006) for a more complete description of the methods and analyses. To access data used in our SN and BNST analyses, visit our [study](https://portals.broadinstitute.org/single_cell/study/SCP466) on the
-Single Cell Portal. 
+Check out our [Cell paper](https://doi.org/10.1016/j.cell.2019.05.006) for a more complete description of the methods and analyses. To access data used in our SN and BNST analyses, visit our study "SCP466" on the
+[Single Cell Portal](https://singlecell.broadinstitute.org/single_cell). 
 
 LIGER can be used to compare and contrast experimental datasets in a variety of contexts, for instance: