An asterisk after the method name (scANVI and scGen) indicates that, in addition, cell identity information was passed to this method. For ComBat and MNN, usability and scalability scores corresponding to the Python implementation of the methods are reported (Scanpy and mnnpy, respectively). ...
recovered 60% and 70%, respectively. However, ddSEQ recovered a significantly lower number of DARs from the consensus DAR set (40%; Fig.3f). Across all eight individual ddSEQ samples, DARs were also positioned closer to TSSs than in all other techniques (Fig.2jand Extended Data Fig.4c). ...
implementation of each GPU module, namedggml-metal.m(Objective C) andggml-cuda.cu(Nvidia C). llamafile embeds those source files within the zip archive and asks the platform compiler to build them at runtime, targeting the native GPU microarchitecture. If it works, then it's linked with ...
ComBat was run in python using Scanpy v1.8.1, MNN was run in R using Batchelor v1.8.0, and Scanorama was run in python using Scanorama v1.7.2. Batch effect correction evaluation To evaluate batch effect correction methods on combined spliced and unspliced modalities, we consider three ...
python-package Cleanup gpu_hist in Python tests. (#11402) Apr 15, 2025 src Allow fallback for CUDA virtual memory. (#11391) Apr 19, 2025 tests Allow fallback for CUDA virtual memory. (#11391) Apr 19, 2025 .clang-format Require context in aggregators. (#10075) Feb 28, 2024 .clang-...
Cell Ranger [15] Python/R Cell Ranger constructs a sparse k-nearest neighbors (kNN) graph where cells are linked if they are among the k nearest Euclidean neighbors. The Louvain modularity optimization algorithm is used to find highly connected modules in the graph. Then, hierarchical clustering...
in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome ...
The article describes thesingle linked list ADT and its traversal implementation. Submitted byRadib Kar, on October 21, 2018 Single linked list Single linked listcontains a number of nodes where each node has a data field and a pointer to next node. The link of the last...
The original implementation comes with CPU but not GPU acceleration while ours is enhanced with GPU support. The SpaGCN and STAGATE with GPU is the implementation in our DANCE. a SpaGCN model in spatial domain identification task. b STAGATE model in spatial domain identification task Full size...
Inter- and intra-tumor heterogeneity is considered a significant factor contributing to the development of endocrine resistance in breast cancer. Recent advances in single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) allow