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Automated CRISPR Screen Analysis

Team workflow Test on crispr-tools.lan or your own dev server, then push to GitHub main.

Data Inputs

Mode

Arrayed Pooled

Data root Raw dir/file

Layout CSV

Genomics XLSX

Output dir Skip FRET Skip GLO Heatmap plate selector (compatibility)

Control Well Selector

Validate first, then either run the whole pipeline or trigger individual stages below.

Idle

Validation has not been run yet.

Guidance

Mode: switch between arrayed and pooled workflows from the same run button.
Auto-fill Paths auto-fills raw/layout/genomics candidates.
Upload Folder/File sends browser-selected inputs to the server and fills the matching path automatically.
Validate Inputs checks that the uploaded or typed files match the expected pipeline format before a run starts.
Raw dir/file: arrayed mode expects a folder (or one raw file); pooled mode expects one pooled table file.
Layout CSV: arrayed mode only; should include plate/well/control metadata columns.
Genomics XLSX: required for arrayed mode, optional for pooled mode.
Skyline sheet is auto-selected internally from compatible worksheets.
Skyline sublibrary is now a dropdown in the interactive skyline figure controls.
Heatmap: exported as one long figure containing all complete plates, one row per plate with three panels (replicate 1, replicate 2, rep1 - rep2).
Heatmap plate selector is retained for compatibility, but current export behavior is all plates.
Difference panels use their own color scale (separate from raw-value scales).
When multiple heatmap plates are selected, one combined SVG is exported containing all requested plates, each with rep1/rep2/diff panels.
Outputs are written to output_dir and output_dir/figures.
For stable long runs, start uvicorn without --reload (auto-reload can restart server mid-run).

No figures shown yet.

Run the pipeline to generate and display new figures.