tag:github.com,2008:https://github.com/carmonalab/scGate/releases 2025-04-24T13:13:11Z tag:github.com,2008:Repository/395000005/v1.7.0 2025-04-24T14:07:44Z <p>New in this version:</p> <ul> <li>Update maintainer email</li> <li>Bug fixes</li> </ul> mass-a tag:github.com,2008:Repository/395000005/v1.6.2 2024-05-13T07:58:37Z <p>New in this version:</p> <ul> <li>Enable parallelization over a list of scGate models (in multi-classifier mode)</li> <li>Fix bug on parallelization when specifying BPPARAM</li> <li>Added cell ontology links for controlled cell type dictionary</li> <li>Update accessor functions to improve compatibility with Seurat v5</li> </ul> mass-a tag:github.com,2008:Repository/395000005/v1.6.0 2023-11-27T12:01:59Z <p>New in this version:</p> <ul> <li>Addresses compatibility with Assay5 Seurat assays.</li> <li>Enables parallelization over a list of models, in multi-classifier mode (see <code>BPPARAM</code>)</li> <li>Uses new implementation of <code>UCell::SmoothKNN()</code> to smooth signature scores between neighboring cells. Neighbor cells are weighted by <math-renderer class="js-inline-math" style="display: inline-block" data-run-id="93dc78992680a4a3b53bba31c23f4ff2">$(1-smooth.decay)^n$</math-renderer>, where n is the n-th neighbor in PCA space, and <code>smooth.decay</code> is a parameter between 0 and 1.</li> </ul> mass-a tag:github.com,2008:Repository/395000005/v1.4.1 2022-12-21T09:34:21Z <p>New in this version:</p> <ul> <li>scGate is now on <a href="https://cran.r-project.org/web/packages/scGate/index.html" rel="nofollow">CRAN</a>! it can be installed using <code>install.packages("scGate")</code></li> <li>The function <code>get_scGateDB()</code> now writes to <code>tempdir()</code> by default. To recover the behavior of previous versions, set <code>destination="./scGateDB"</code> or to some other local directory</li> <li>Log out fraction of "Pure" cells instead of "Impure" cells</li> <li>Fixed bug on kNN smoothing with too few remaining cells</li> <li>Improved documentation and examples</li> </ul> mass-a tag:github.com,2008:Repository/395000005/v1.2.0 2022-07-29T14:05:36Z <p><strong>New features in version 1.2.0</strong></p> <ul> <li>Simultaneously evaluate <strong>multiple gating models</strong>, given as a list to <code>model</code> parameter <ul> <li>Returns individual gatings as well as a combined cell type annotation from all the models (<em><strong>scGate_multi</strong></em> metadata column)</li> <li>Allows running scGate as a multi-class classifier and annotate cell types in a dataset</li> </ul> </li> <li><strong>New <code>reduction</code> parameter</strong> <ul> <li>Allows nearest-neighbor smoothing on an existing dimensionality reduction (e.g. "pca" or "harmony")</li> <li>Can significantly speed up computation time and annotation of integrated objects</li> </ul> </li> <li>Uses Bioconductor version of <a href="https://bioconductor.org/packages/release/bioc/html/UCell.html" rel="nofollow">UCell</a></li> </ul> mass-a tag:github.com,2008:Repository/395000005/v1.0.1 2022-02-21T12:20:13Z No content. sjcarmona tag:github.com,2008:Repository/395000005/v1.0.0 2021-11-03T14:27:38Z <p>First stable release of scGate</p> mass-a