Comments (3)
Avsecz
commented on June 14, 2024
Thanks! Could you send a pull-request for that patch or a generalization of it? Happy to merge it. I've only been working with double-stranded data so many of the tools, especially the downstream interpretation ipython notebooks will only work with double-stranded data.
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snystrom
commented on June 14, 2024
Sure. Although I'm not sure the best way to detect whether there are any negative predictions. I haven't spent a ton of time digging into your API, so not sure the best way to make this work for both use cases.
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Avsecz
commented on June 14, 2024
Added the fix here: b9ec3e9. LMK if that doesn't solve the issue.
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Related Issues (20)
- AttributeError: 'str' object has no attribute 'decode' error in bpnet contrib HOT 6
- Normalizing by SeqLen in Profile Loss HOT 2
- BED file with strands HOT 2
- examples file snakefile HOT 1
- installation problem
- bpnet installation problem HOT 1
- Bpnet Added Channels Leads to Profile Predictions of 0
- Empty batch error loading training data into memory HOT 5
- Error when traning ATAC-seq with one track
- bpnet contrib function error
- Viewing the hypothetical impscores HOT 2
- contrib.counts vs contrib.profile HOT 2
- OverflowError: can't convert negative value to CHRPOS
- examples/recommendations for ATAC/Dnase-seq data HOT 4
- preds.neg.bw and preds.pos.bw
- running bpnet cwm-scan modisco HOT 2
- Error building Leidenalg wheel in Colab environment
- Notebook not working HOT 2
- Installation error, likely crashing due to dependency DeepExplain
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