BD Cellismo^™ Data Visualization Tool

新增功能

• 支持 BD Rhapsody™ TCR/BCR Next 多组学
  1. 新增AIRR分析模态，兼容符合AIRR标准的重排TSV文件与仅VDJ 数据集
  2. 支持多组TCR/BCR数据集的合并与分析
  3. 支持修改分析流程（BD pipeline）默认提供的细胞类型注释，以指定用于TCR/BCR分析的细胞
  4. 支持自定义克隆型与克隆扩增注释分类
  5. 支持查看克隆型大小分布与丰度图
  6. 通过可检索表格、交互式蜂窝图与柱状图探索克隆型；支持按细胞注释或基因表达量着色，并筛选排名靠前的克隆型
  7. 在整个软件中，可将克隆型定义作为细胞注释，例如：
     • 跨克隆型开展差异表达分析
     • 通过热图、直方图与小提琴图对比不同克隆型之间的基因表达差异
     • 在降维图上展示特定克隆型
  8. 查看同一克隆型下contig的核苷酸/氨基酸序列多序列比对结果，并支持FASTA格式导出
  9. 支持在不同分类注释之间，比较克隆型重叠度，优势克隆/选定克隆的频率变化
  10. 支持在不同的分类注释之间，比较免疫组库的多样性、丰富度与优势克隆占比
  11. 支持查看单个与联合基因片段使用情况，包括配对链的使用信息
  12. 支持查看CDR3长度分布与序列基序特征
  13. 支持B细胞谱系示踪分析
• 整体质量控制：新增ATAC数据的峰内转座酶位点占比、TSS富集分数与核小体信号得分等质控指标

更新内容

• 更新最终用户许可协议

问题修复

• 双细胞检测：修复重新运行后细胞误删问题
• 双轴图：修复在已有细胞注释内新建注释分类时出现的界面卡死问题
• 双轴图：修复未打开项目时选择坐标轴触发的界面死问题

Added:

• Trajectory analysis utility tool using PAGA
• Cell Cycle analysis utility tool
• ATAC Browser: Gene/peak correlation track with arcs colored by correlation score
• ATAC Browser: Added an RNA expression violin plot, enabling combined view of a gene's genomic region and expression
• Stacked Bar new graph type—view categorical annotations stacked vertically and optionally split by a second categorical annotation. Useful for cell type proportion analysis and more
• Biaxial Graph: Added hexbin density visualization
• Biaxial Graph: Added numerical annotations as options for X and Y axis
• Bioproduct Correlation Graph: Added 'scaled sum' aggregation type, to correct for differences in cell number between categories
• Export Format: Added export for ATAC modalities to the HDF5 format to enable Seurat import
• Export Format: Added ability to split CSV and FCS exports to individual files by any categorical cell annotation
• Application update notifications and built-in streamlined update mechanism
• Optional anonymous telemetry to help us improve the product. Does not transmit any single-cell data

Updated:

• Continuous color palette selector shows the color range during selection
• ATAC Browser: optimized reloading and redrawing operations to make usage faster
• ATAC Browser: settings sidebar can be collapsed
• ATAC Motif Enrichment: motif logos added to the table of results
• Bioproduct Correlation Graph: Updated aggregation functions to always operate on the linear scale
• Classify Cell Types: allow overwrite of an existing cell annotation
• Dimensionality Reduction Graph:  Updated legend to allow selection cells from categorical annotation labels
• Project Start: Improved speed of import for Seurat objects

Fixed:

• Violin and Histogram graphs: fixed errors when using 'Deselect all' categories
• Project Start: H5MU import—modalities that are not recognized are ignored

Added:

• ATAC Browser: Transcription Start Site track

Updated:

• ATAC Browser: Better performance by caching data

Fixed:

• Doublet Detection or QC Remove Categorical: Removing cells by these mechanisms causes the bioproduct list to fail, displaying "Object:object" until the project is reloaded
• Start Project: ATAC Fragment file merging can fail when loading two or more ATAC-Seq datasets that used a custom reference genome
• ATAC Browser: Better handling of chromosome names from custom species reference 
• Differential Analysis: Method DESeq2 failure

Added: 

• Support for BD Rhapsody™ ATAC-Seq Assay
  • New modalities: ATAC_PEAKS, ATAC_GENE_ACTIVITY, ATAC_MOTIF
  • Genome browser to view ATAC peaks and ATAC fragments in the context of genomic locations and genes
  • Motif enrichment analysis tool—find transcription factor motifs that are enriched in a given set of peaks, compared to background peaks
  • Peak and RNA expression correlation tool—find peaks whose activity correlate with RNA expression
  • RNA vs ATAC heatmap—see RNA expression and ATAC gene activity correlation for a given cell annotation
  • Ability to combine and reanalyze multiple ATAC datasets
• Doublet detection tool
• Batch correction utility tool, with batch correct counts available to be used in graphing pages
• Integration utility tool
• New cell classification tool, ScType, with the ability to customize marker genes
• Confidence score annotations for cell type classification tools
• Project action recording on the current project page
• Data export options—for R / Seurat, Scanpy (H5AD), Muon (H5MU), FCS and CSV
• RNA data import option—Seurat RDS
• New DESeq2 method in the Differential Analysis tool
• "Selected Cell Actions" menu on graphing pages, and added "Delete Cells" and "Quick Differential Analysis" options
• Switch to reverse color palette
• Contour lines overlay to biaxial plot
• Options to start project, including flavor of highly variable gene selection, number of highly variable genes and number of PCA/LSI components
• Ability to filter bioproduct dropdown by modality
• Ability to Export and restore app settings