Software
- Can you give more information on the statistical test used for differential expression analysis in Cell Ranger?
- How can I replicate the t-SNE plot in Loupe Cell Browser?
- How do I prepare Sequence Read Archive (SRA) data from NCBI for Cell Ranger?
- How does Cell Ranger auto-detect chemistry?
- How is sequencing saturation calculated?
- Are the "Mean UMI Counts" from differential expression analysis normalized?
- Can you repeat cell-calling without re-running cellranger count?
- How can we add genes to a reference package for Cell Ranger?
- How does Cell Ranger process and filter UMIs?
- What version of STAR is used in Cell Ranger?
- How can I create categories in the .cloupe file from cellranger aggr?
- Gene Table in Loupe Browser highlight up-regulated genes by default?
- How can I regress certain genes such as cell cycle genes?
- How are the UMI counts normalized before PCA and differential expression?
- What is a barcode whitelist?
- What are valid barcodes?
- What parameters are used for STAR index?
- How does cellranger aggr normalize for sequencing depth among multiple libraries?
- What does "ERROR; return code from pthread_create() is 11" mean?
- How does Cell Ranger correct for amplification bias?
- How were SNVs called in this paper: Massively parallel digital transcriptional profiling of single cells
- How does Cell Ranger correct barcode sequencing errors?
- Which reads are considered for UMI counting by Cell Ranger?
- What contributes to a low transcriptome mapping rate in Cell Ranger?
- Files and criteria used to generate 10x references?
- Can I run Cell Ranger on my Mac or Windows machine?
- How does cellranger count identify multiplets?
- How are barcodes classified as cell-associated?
- Can I aggregate gene expression data from different chemistries ?
- Can low abundance transcripts be detected?