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Hi @kexinhuang12345, as you know `ReplogleWeissman2022` study has three datasets.
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Currently, as I understand `ReplogleWeissman2022_K562_gwps` data is not uploaded. However, I noticed a wei…
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Hi everyone,
I just realized that my Snakemake pipeline step 3 isn't starting because of the ranking and score database. It seems that every time I download the ranking and the scores database from…
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Hi,
As far as I can see, kindr implements only a boxPlus operation for global perturbations, i.e.
Phi_2 = exp(v)*Phi_1
Do I overlook something or would it (maybe) make sense to add a boxPlusLocal ope…
hdino updated
6 years ago
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According to [custom data turorial](https://github.com/snap-stanford/GEARS/blob/master/demo/data_tutorial.ipynb),
> (2) Create your own Perturb-Seq data
Prepare a scanpy adata object with
adat…
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Perturbations where we perform -resid_acts vs when we don't should be distinguished and both be accessible by specifying a parameter (for example).
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Hi @forever208 ,
Great work! I like your observation of the inconsistency between training and sampling and propose a simple input perturbation to mitigate/align it. A question about your implementat…
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GO:0052026 'symbiont-mediated perturbation of host transcription'
GO:0019056 modulation by virus of host transcription
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The Simultaneous Perturbation Stochastic Approximation (SPSA) optimisation method is a faster optimisation method.
> If the number of terms being optimized is p, then the finite-difference method…
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Instead of just having a fixed tidal spinup, use the spin up with all forcing all the way to the point where we start perturbing the track.
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Where can I generate or get the `perturbation_constraint_pca0.8_100.pkl` file?