Analysis scripts assciated with manuscript:

Finnegan A. et al."Single-cell transcriptomics reveals spatial and temporal turnover of keratinocyte differentiation regulators."

codes — custom codes used for analyis

• Single-cell imputation
  • ./codes/run_zinb.R
  • ./codes/run_MAGIC.py
• Dimensionality reduction and cell clustering
  • ./codes/cluster_spectral.py and ./codes/run_specCluster.py
  • ./codes/run_PCA.py
• Differential expression
  • ./codes/fantomDE.py
  • ./codes/run_cluster_DE_subsetCells.R
• Differential motif enrichment
  • ./codes/rankMotifs.py
  • ./codes/diffEnrich_motifs.py
• Identification of gene and TF modules
  • ./codes/corrFuncs.py and /codes/run_calcCorr.py
  • ./codes/run_clusterCoRegTFcorr.py
  • ./codes/run_getClustMapBlocks_inconsistStat.py
• Transcriptomic comparison of single-cell population with bulk BCC/SCC samples
  • **Fill in**
• And other miscellaneous scripts

Analysis and generation of results

• getTFCandidates — Constructs sets of candidate transcription regulators based on specificity of expression across primary cells

• imputeExpr —scripts for imputation of single cell expression from raw counts

• clusterCells — dimensionality reduction and clustering cells into 8 stages based on imputed expression values

• DE — One vs rest test for genes differentiatlly expressed in each stage. Tests for genes differentiatlly expressed between the BK and DK state

• exprCorr — Calculation of gene expression correlations across cells in various combinations of stages

• motifAnalysis — Identification of TF binding motifs differentially enriched between SEs unique fo the BK and DK states

• TFexpr_bindingMoitf_assn — Association between coordinated changes in TF expression and differential binding enrichment between super-enhancers specific to BK and DK states

• regNetwork — Identification of gene and TF modules based on expression correlation

• antiox — Analysis of expression of genes annotated for antioxidant function across progressive differentiation stages

Misc

• ./raw — contains files that are starting points for analysis.

• ./setsGenes — Gene sets generated during analysis