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Jonathan J. Froehlich
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Quantitative gene regulation
Analysis workflows
ATAC-seq
scRNA-seq
MPRA
Code and data connections between analysis workflows
A shared transcription-factor perturbation connects three experimental avenues. Each avenue has its own processing and analysis workflow, with selected ATAC, single-cell RNA and MPRA data products exchanged between repositories.
TF perturbation & dose
FACS · RT-qPCR
Reads, peaks & tracks
alignment · QC · peak calling
Response & sequence evidence
DiffBind · ChromBPNet · motifs
Peak response & grammar
dose response · regulatory grammar
Counts, multiplexing & QC
STARsolo · MULTI-seq · cell QC
Expression dose response
pseudobulk · DESeq2 · curves
Gene programs & motifs
enrichment · promoters · alleles
Library construction
candidates · controls · oligo QC
Barcode assignment & counts
CRE lookup · DNA/RNA matrices
Activity & dose response
BCalm · curves · ATAC comparison
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