Software
- How is "Log2 Fold Change" calculated?
- Which genes are displayed in the Loupe Cell Browser heatmap?
- How to fix Loupe Cell Browser error "Empty barcode list supplied"?
- How to resolve mkref error: BUG: next index is smaller than previous, EXITING
- How can I aggregate or compare single-cell libraries between species?
- Are there methods for identifying multiplets?
- Are there other methods for calling barcodes as cell-associated?
- Why does cellranger aggr fail with "Your header row is missing a required field: library_id."?
- Where are the STAR alignment logs from cellranger count?
- How can I identify the 10x library sources when analyzing an aggr matrix using Seurat?
- Do you have the cell-type annotations for the 1.3M mouse brain cells dataset?
- How can I identify cells that express Gene A but not Gene B in Loupe Cell Browser?
- Why did cellranger count fail in the CHUNK_READS stage?
- How do you select the number of PCs to use for clustering and t-SNE?
- How do you decompress the 2-bit barcode sequences in molecule_info.h5 file?
- How can I color the t-SNE plot based on graph-based clustering in cellrangerRkit?
- Can I generate a 3D t-SNE plot from Cell Ranger output?
- How to interpret the "Fraction Reads in Cells" metric?
- How can I modify the STAR alignment parameters in Cell Ranger?
- What is the relationship between principal components (PCA) and genes?
- Can I generate a matrix h5 file from a molecule_info.h5 file?
- How can I get an updated filtered gene-barcode matrix after running cellranger reanalyze with --force-cells?
- Why does a warning from cellranger mkref point to an empty list?
- How can I get read counts for the observed UMIs?
- How can I color the t-SNE plot by 10x library in cellrangerRkit?
- What is the AN tag in the BAM file from cellranger count?
- How can I customize the parameters for k-means and graph-based clustering in Cell Ranger?
- How can I customize the parameters for t-SNE in Cell Ranger?
- How can I customize the parameters for PCA in Cell Ranger?
- Why is Cell Ranger failing in stage code with exit status 1 in cluster mode?