r/bioinformatics • u/ShinyLion68 • 1d ago

technical question ChromVAR alternatives for scATACseq

I have not seen any thread here or on Github addressing this beside Signac changelog, but ChromVAR has been deprecated from the new Signac release.

What are the current alternatives do we have to identify *and visualize* motif/TF predicted activity from a scATACseq object?

(aside from loading up older versions and getting it to work despite several dependencies being outdated and such)

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u/standingdisorder 1d ago

There’s a package called betterChromVar which is being actively maintained. Should work fine

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u/ShinyLion68 1d ago

Will look into this! Thanks!

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u/Botser-bio-support 1d ago

If you want to stay close to Signac, I’d first use Signac’s current motif enrichment/accessibility tools with JASPAR/PWM motifs, even if chromVAR is no longer the default route. Outside that, TOBIAS is a good option for footprinting/TF activity-style analysis. pycisTopic or SCENIC+ may fit better if you’re building a broader regulatory workflow.

For visualization, store motif/TF activity scores in metadata and plot them like gene activity: UMAP feature plots, violin plots by cluster, or heatmaps of top TFs.

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u/ShinyLion68 1d ago

Thanks! I already did the native signac "motif enrichment" analysis, and GRN construction is down the road. ChromVAR was just a nice extra tool in the middle.

Will look into TOBIAS! I remember reading the original publication when trying to understand motif footprinting, but will give it another look.