Context: Domain: single-cell transcriptomics; Study: Human γδ T cells dataset with 7417 cells and 35477 genes. Dataset contains γδ T cells from various tissues and development stages with metadata including tissue type, classification, donor information, and cell type annotations.

Question: Calculate the Silhouette coefficient for tissue-based clustering using harmony-corrected PCA embeddings. Use the first 30 principal components and tissue as the ground truth labels. What is the mean Silhouette coefficient rounded to 4 decimal places?
Answer guideline: Answer must be a numeric value rounded to 4 decimal places (e.g., 0.1234).
Answer: 0.0305
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Question: Perform differential expression analysis between 'Naive' and 'Effector' classification groups using Wilcoxon rank-sum test. Among genes with adjusted p-value < 0.01 and absolute log2 fold change > 1, how many genes are upregulated in Effector cells compared to Naive cells?
Answer guideline: Answer must be a single numeric value (e.g., 42) with no units or text.
Answer: 39
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Question: Calculate the Jensen-Shannon distance between gene expression distributions of cells from 'blood' vs 'lung' tissues. Use only the top 1000 most variable genes and normalize expression values to probabilities. What is the Jensen-Shannon distance rounded to 4 decimal places?
Answer guideline: Answer must be a numeric value rounded to 4 decimal places (e.g., 0.1234).
Answer: 0.0668
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Question: Calculate the entropy of the Vδ chain usage distribution weighted by donor frequency. For each donor, calculate the Shannon entropy of their Vδ chain distribution, then compute the mean entropy across all donors. What is the mean entropy rounded to 4 decimal places?
Answer guideline: Answer must be a numeric value rounded to 4 decimal places (e.g., 0.1234).
Answer: 1.1907
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Question: Perform trajectory inference using PAGA (Partition-based graph abstraction) with Leiden clustering at resolution 0.5. Calculate the connectivity between 'Naive' and 'Memory' classification groups, using 2000 hvgs and 15 neighbors with 30 pcs when random state is 42). What is the PAGA connectivity value between these groups rounded to 4 decimal places?
Answer guideline: Answer must be a numeric value rounded to 4 decimal places (e.g., 0.1234).
Answer: 0.6795
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Question: Calculate the batch effect strength using kBET (k-nearest neighbor batch effect test) on the harmony-corrected PCA space using donor_id as batch variable. Use k=15 neighbors and alpha=0.05. What percentage of cells reject the null hypothesis of no batch effect (rounded to 2 decimal places)?
Answer guideline: Answer must be a numeric value rounded to 2 decimal places (e.g., 12.34).
Answer: 90.99
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Question: Calculate the Local Inverse Simpson Index (LISI) for donor integration in the harmony-corrected PCA space. Use k=30 neighbors and evaluate how well donor identities are mixed. What is the mean donor LISI score rounded to 4 decimal places?
Answer guideline: Answer must be a numeric value rounded to 4 decimal places (e.g., 0.1234).
Answer: 2.8550
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Question: Perform gene set enrichment analysis (GSEA) on differential genes between 'fetal' and 'adult' development stages using the Hallmark gene sets. Among significantly enriched pathways (FDR < 0.05), how many are upregulated in adult compared to fetal cells?
Answer guideline: Answer must be a single numeric value (e.g., 42) with no units or text.
Answer: 0
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Question: Compute cell-cell communication potential using CellPhoneDB methodology by testing the provided ligand-receptor pairs (TNF_TNFRSF1A, TNF_TNFRSF1B, IL6_IL6R, IL1B_IL1R1) with 10 permutations, counting significant interactions (p < 0.05) between different classification groups in each tissue, and report the maximum number observed in any single tissue.
Answer guideline: Answer must be a single numeric value (e.g., 42) with no units or text.
Answer: 0
Source paper: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span