human pbmc dataset  (10X Genomics)

Journal: bioRxiv

Article Title: Chromap Suite: an open-source single-binary platform for agentic multiomic RNA + ATAC profiling

doi: 10.64898/2026.06.02.729736

Figure Lengend Snippet: Standalone wall-clock (left) and peak resident memory (right) at T = 1, 4, 24 threads versus single-threaded MACS3 v3.0.3 on the public 10x 3K PBMC Multiome ATAC channel (53.97 M deduplicated fragments). Speedup ratios annotated above libMACS3 bars. All thread counts produce a 50,274-peak narrowPeak file byte-identical to the MACS3 v3.0.3 reference; treat, lambda, and ppois bedGraphs and summit calls are likewise byte-identical (see Methods, ).

Article Snippet: The source code described in this work is freely available under permissive open-source licences: The 10x Genomics 3K PBMC Multiome dataset used for benchmarking is publicly available from 10x Genomics [ ].

Techniques:

Journal: bioRxiv

Article Title: CellClick: an interactive platform for adjustable and accurate cell type annotation in single-cell and spatial omics data

doi: 10.64898/2026.06.01.727775

Figure Lengend Snippet: (A) The schematic diagram of the cell identification workflow for the 10k PBMCs dataset using CellClick. CD14+ Mono, CD14 + Monocytes; MAIT, mucosal-associated invariant T cells; NK, natural killer cells; CD16+ Mono, CD16 + Monocytes; pDC, plasmacytoid dendritic cells. (B) Reference marker gene-based marker gene scores for Cluster “0” and Cluster “6”. (C) Expression patterns of CellClick suggested marker genes for Cluster “0” and Cluster “6”. (D) Annotation results for Cluster “0” and Cluster “6” using CellClick. (E) Reference marker gene-based marker gene scores for Cluster “5”. Reference marker genes with ambiguous cell type identities are highlighted with red box in the dot plot. (F) Expression patterns of CD3D (the marker gene for T cells), CD8B (the marker gene for CD8 + T cells), NCR1 (the marker gene for NK cells), and NCAM1 (the marker gene for NK cells) across all cell clusters. (G) Annotation results for Cluster “5” using CellClick. (H) UMAP embedding showing cells expressing SLC4A10 in the 10k PBMCs dataset. (I) UMAP embedding of cell selection results for Cluster “MAIT” using the Cluster Refinement function. (J) Newly identified marker genes for temporary Cluster “MAIT,0” and Cluster “MAIT,1” after rerunning the Cell Identification function. (K) Reannotation results for Cluster “MAIT” using CellClick. The color rule for gene names in the dot plots of panels (C) and (E) is the same as described in (C) .

Article Snippet: The 10k PBMCs dataset, a human peripheral blood single-cell RNA-seq dataset, was downloaded from the 10x Genomics website ( https://www.10xgenomics.com/cn/datasets/10-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0 ) and used to demonstrate the ability of CellClick in generating more accurate cell type annotation results for preprocessed single-cell RNA-seq dataset.

Techniques: Marker, Expressing, Selection

Journal: bioRxiv

Article Title: CellClick: an interactive platform for adjustable and accurate cell type annotation in single-cell and spatial omics data

doi: 10.64898/2026.06.01.727775

Figure Lengend Snippet: (A) Workflow and functions of the Data Preprocessing module. (B) Workflow and functions of the Data Visualization module. (C) Workflow and functions of the Cell Annotation module. In the dot plot of the Cell Identification function, the names of known reference marker genes reported by COSG are shown in red, and the names of marker genes newly identified by COSG are shown in blue. (D) Workflow and functions of the Annotation Validation module. The dot plot produced by the Reference Comparison function shows the expression pattern of marker genes identified for the target cluster, sorted by their COSG scores. (E) Workflow and functions of the Cell Reannotation module. Panels (B) to (E) represent the analysis results of the 3k PBMCs dataset.

Article Snippet: The 3k PBMCs dataset, a human peripheral blood single-cell RNA-seq dataset, was downloaded from the 10x Genomics website ( https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.1.0/pbmc3k ) and used to illustrate the main functions of CellClick.

Techniques: Marker, Biomarker Discovery, Produced, Comparison, Expressing

Journal: bioRxiv

Article Title: CellClick: an interactive platform for adjustable and accurate cell type annotation in single-cell and spatial omics data

doi: 10.64898/2026.06.01.727775

Figure Lengend Snippet: (A) The schematic diagram of the cell identification workflow for the 10k PBMCs dataset using CellClick. CD14+ Mono, CD14 + Monocytes; MAIT, mucosal-associated invariant T cells; NK, natural killer cells; CD16+ Mono, CD16 + Monocytes; pDC, plasmacytoid dendritic cells. (B) Reference marker gene-based marker gene scores for Cluster “0” and Cluster “6”. (C) Expression patterns of CellClick suggested marker genes for Cluster “0” and Cluster “6”. (D) Annotation results for Cluster “0” and Cluster “6” using CellClick. (E) Reference marker gene-based marker gene scores for Cluster “5”. Reference marker genes with ambiguous cell type identities are highlighted with red box in the dot plot. (F) Expression patterns of CD3D (the marker gene for T cells), CD8B (the marker gene for CD8 + T cells), NCR1 (the marker gene for NK cells), and NCAM1 (the marker gene for NK cells) across all cell clusters. (G) Annotation results for Cluster “5” using CellClick. (H) UMAP embedding showing cells expressing SLC4A10 in the 10k PBMCs dataset. (I) UMAP embedding of cell selection results for Cluster “MAIT” using the Cluster Refinement function. (J) Newly identified marker genes for temporary Cluster “MAIT,0” and Cluster “MAIT,1” after rerunning the Cell Identification function. (K) Reannotation results for Cluster “MAIT” using CellClick. The color rule for gene names in the dot plots of panels (C) and (E) is the same as described in (C) .

Article Snippet: The 3k PBMCs dataset, a human peripheral blood single-cell RNA-seq dataset, was downloaded from the 10x Genomics website ( https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.1.0/pbmc3k ) and used to illustrate the main functions of CellClick.

Techniques: Marker, Expressing, Selection