1.1.0

• On cumulus workflow:
  • Add CITE-Seq data analysis back. (See section Run CITE-Seq analysis for details)
  • Add doublet detection. (See infer_doublets, expected_doublet_rate, and doublet_cluster_attribute input fields)
  • For tSNE visualization, only support FIt-SNE algorithm. (see run_tsne and plot_tsne input fields)
  • Improve efficiency on log-normalization and DE tests.
  • Support multiple marker JSON files used in cell type annotation. (see organism input field)
  • More preset gene sets provided in gene score calculation. (see calc_signature_scores input field)
• Add star_solo workflow (see STARsolo section for details):
  • Use STARsolo to generate count matrices from FASTQ files.
  • Support chemistry protocols such as 10X-V3, 10X-V2, DropSeq, and SeqWell.
• Update the example of analyzing hashing and CITE-Seq data (see Example section) with the new workflows.
• Bug fix.