PR: https://github.com/theislab/hadge/pull/67 Script 1: Basic Demultiplexing Merger Combines results from two demultiplexing approaches: • Input: Takes genetic and hashing demultiplexing output folders • Processing: Finds assignment and classification CSV files, merges them by barcode, and applies standard label mappings (DBL→doublet, AMB→negative, SNG→singlet) • Output: Creates merged assignment and classification files combining both approaches Script 2: Genetic Demultiplexing Pipeline Processes multiple genetic demultiplexing tools (Demuxlet, Freemuxlet, Vireo, Souporcell, scSplit): • Input: Each tool's output folder contains barcode assignments and method parameters • Processing: Each tool has a specific parser that extracts donor assignments and classifications from different file formats (.best files, .tsv files, etc.) • Data Integration: Optionally creates AnnData/MuData objects with the assignments for downstream analysis • Output: Individual tool results plus merged files combining all genetic methods Script 3: Hashing Demultiplexing Pipeline Processes hashtag antibody (HTO) demultiplexing results from multiple tools (demuxem, hashsolo, hashedDrops, multiseq, htodemux, GMM-Demux, BFF): • Input: Each tool produces different output formats (some with confidence scores, some with probability matrices) • Processing: Tool-specific parsers handle the varied output formats and map results to standard labels (singlet/doublet/negative) • Special Cases: Some tools like GMM-Demux require complex config file parsing to determine hashtag counts • Output: Similar to script 2 - individual results plus merged files

I'll gladly take any stones into my face for my LLM usage but it should be accurate in this case.

Does anyone have an example file of

hash_summary/hashing_assignment_all.csv

or

hash_summary/hashing_classification_all.csv

for me?

assignment_all.to_csv("hash_summary/hashing_assignment_all.csv", index=False)  
classification_all.to_csv("hash_summary/hashing_classification_all.csv", index=False)

from here: https://github.com/theislab/hadge/blob/feature/improve_python_scripts/bin/summary_hash.py

Does anyone have an example file of

hash_summary/hashing_assignment_all.csv

or

hash_summary/hashing_classification_all.csv

for me?

This ZIP should contain everything you need