Rahul Satija

Jul 18, 2024 | genomebiology.biomedcentral.com | Alsu Missarova |Emma Dann |Leah Rosen |Rahul Satija

miloDE is a cluster-free framework for differential expression (DE) testing that leverages a graph representation of scRNA-seq data (Fig. 1). To construct a graph recapitulating distances between cells, we require count matrices and a pre-calculated joint latent embedding across all the replicates from tested conditions (Fig. 1, step 1).

Jan 12, 2024 | biorxiv.org | Austin Hartman |Rahul Satija

AbstractThe burgeoning interest in in situ multiplexed gene expression profiling technologies has opened new avenues for understanding cellular behavior and interactions. In this study, we present a comparative benchmark analysis of six in situ gene expression profiling methods, including both commercially available and academically developed methods, using publicly accessible mouse brain datasets.

Aug 17, 2023 | cell.com | Mohammad Lotfollahi |Fabian J. Theis |Rahul Satija

GlossaryMultimodal reference: a reference atlas that is built using more than one modality (for example, RNA and ATAC). Multimodal omics: technologies capable of capturing multiple data types from the same sample. Supervised vs. unsupervised learning: in this context, data integration while leveraging cell-type labels in the reference and query dataset (supervised) compared with the scenario in which the method has no access to these labels (unsupervised).

Jul 19, 2023 | nature.com | Seth Winfree |Qiwen Hu |Ricardo Melo Ferreira |Daria Barwinska |fei chen |Sushrut S. Waikar | +12 more

Statistics and reproducibilityFor 3D imaging and immunofluorescence staining experiments, each staining was repeated on at least two separate individuals or separate regions. For immunofluorescence validation studies, commercially available antibodies were used; 13 out of the 15 tissue samples were also analysed using snCv3 or scCv3. For ISH, 6 tissue samples (4 biopsies and 2 nephrectomies) were analysed.

Jun 6, 2023 | nature.com | Zhiliang Bai |Rahul Satija

AbstractSingle-cell multi-omics technologies and methods characterize cell states and activities by simultaneously integrating various single-modality omics methods that profile the transcriptome, genome, epigenome, epitranscriptome, proteome, metabolome and other (emerging) omics. Collectively, these methods are revolutionizing molecular cell biology research.