TAM Atlas (Using a pan-cancer atlas to investigate tumour
May 20, 2024 · The atlas is a Seurat (v 4.2.0) object stored as a .rds file, which can be loaded in R (v 4.2.2). Note this atlas does not include raw count data as these can be download from the …
Single-cell spatial transcriptomics (6k-plex CosMx SMI) dataset of ...
Dec 9, 2024 · The dataset is provided as a Seurat object in .rds format, and consists of in situ transcripts for 6075 genes in 232,802 cells + metadata (see Metadata section below).
msigdbr rds - Zenodo
Jul 3, 2025 · Data for msigdbr R package.
Immune-epithelial-stromal networks define the cellular ecosystem …
Apr 22, 2025 · spatial_transcriptomics_zenodo.RDS - Seurat object RDS file with 10x Visium spatial transcriptomics dataset. gamma_delta.RDS - Seurat object RDS file with scRNA-Seq …
Development, evaluation and application of NicheNet: datasets
Jun 28, 2019 · * datasets to demonstrate application possibilities of NicheNet: - pemt_signature.txt: p-EMT geneset for which upstream regulators will be predicted - …
Multi-organ CD45+ immune cell atlas - Zenodo
Dec 29, 2023 · MultiOrgan_MetaAtlas_total_level3_qc.rds: an rds file containing a Seurat object 114275 cells (RNA integrated assays, PCA and UMAP reductions and quality metrics)
Systematic reconstruction of molecular pathway signatures using ...
Dec 18, 2024 · HClust_Pathway_celltype_specific_genelist.rds: The cell-line specific pathway gene lists from hierarchical clustering analysis independently done on each cell line9.
EPICv2 Re-annotated Manifest version 1.0 - Zenodo
Feb 26, 2025 · The other two files (EPICv2_reannotated_manifest_forcomparison_v1.0.csv.zip and EPICv2_reannotated_manifest_forcomparison_v1.0.rds) contain the novel annotation and …
Single cell and spatial analysis of immune-hot and immune-cold …
Dec 5, 2024 · HNSCC_fibroblasts_integ_srt.RDS - Seurat object containing fibroblasts from integrated analysis of EPG dataset (https://cellxgene.cziscience.com/collections/3c34e6f1 …
Mapping spatial organization and genetic cell state regulators to ...
Jul 15, 2024 · Files are provided in the form of RObjects (extension .rds) or tabulated data (extension .csv) to reproduce the results and figures provided in the paper via the the R …