diff --git a/DESCRIPTION b/DESCRIPTION index ea4fcdd..1c855ba 100644 --- a/DESCRIPTION +++ b/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) , and Liu J, Gao C, Sodicoff J, et al (2020) for more details. diff --git a/NEWS.md b/NEWS.md index 1030b82..f3306a5 100644 --- a/NEWS.md +++ b/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 diff --git a/README.md b/README.md index 431519a..45af905 100644 --- a/README.md +++ b/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: