Issues

• Compatibility and recommendations for Stereo-seq data

  raphael-group/CalicoST#31 · Filter by author OMIC-coding opened on May 7, 2026

• confused about the B allele count

  raphael-group/CalicoST#30 · Filter by author lichen2018 opened on Apr 2, 2026

• why the bam files in CalicoST_example, simulated_example, and prostate_example are empty?

  raphael-group/CalicoST#29 · Filter by author lichen2018 opened on Mar 11, 2026

• Providing normal spots when jointly running multiple slices

  raphael-group/CalicoST#28 · Filter by author James-Qiao opened on Jan 23, 2026

• calicoST tumor purity estimation and cna run both end up filtering out all spots

  raphael-group/CalicoST#27 · Filter by author KSimi7 opened on Jan 22, 2026

• Estimate of tumor proportion returns NA for most of the spots

  raphael-group/CalicoST#26 · Filter by author ElyasMo opened on Oct 23, 2025
  1

• Error in estimate purity

  raphael-group/CalicoST#25 · Filter by author palmfern opened on Oct 3, 2025

• Error in parse_final_snp

  raphael-group/CalicoST#24 · Filter by author palmfern opened on Sep 25, 2025
  2

• Qustions about step run CalicoST

  raphael-group/CalicoST#22 · Filter by author vincentguo0418 opened on Apr 27, 2025

• How to get the CN values matrix from results

  raphael-group/CalicoST#21 · Filter by author yanglq-bioinfo opened on Apr 16, 2025

• UnboundLocalError

  raphael-group/CalicoST#18 · Filter by author kzb193 opened on Dec 29, 2024
  6

• compatible scipy version for frequent ".A error" in parse_final_snp.py, utils_IO.py, etc.

  raphael-group/CalicoST#14 · Filter by author wangmengbo opened on Nov 27, 2024

• empty result when using cellsnp-lite

  raphael-group/CalicoST#12 · Filter by author onmyojiyys opened on Nov 11, 2024
  4