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Hello, thanks for developing a really nice tool!
I've ran cellbender remove-background with no issues on multiome data while keeping both Gene Expression and Peaks features. However, I'm currently…
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The threshold feature that is implemented in the following line requires the `lenspack` package, which is not in conda, and must be installed via `pip`. For ease of use with package installs, I will c…
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help for naive users
The root reason I see is that the BED and BAM inputs are not in the "same order". Could we describe this better so users know what to do to address it? Maybe quote back parts o…
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Good morning,
I have a question about filters that have to be applied on differential methylation results. Default filters peaks that have pvalue>0.0001, nevertheless also padj is evaluated. So my qu…
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z_disk) chbmp@UOL-L-P9H6X356VP z_disk % python scripts/pointcloud_to_image.py -x 'Group X Position' -y 'Group Y Position' -z 'Group Z Position' -bs size -hx 50 -hy 50 -hz 50 -s tab
List of files whic…
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Add in a gene name at the most significant peaks (previous/novel loci) 🔶
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Our workflow is findChromPeaks, groupChromPeaks and fillChromPeaks. I am finding duplicate values in the output from fillChromPeaks - I have attached a sample file.
Is this expected behaviour where …
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Given a peak group that contains peaks for samples A, B, and C; in an experiment that also contains samples D and E, apply reextraction protocol to render a reextract peak for samples D and E.
This…
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Hi there.
We noticed 1 to 2 times per day that login lasts around 12s due to agent parsing. This is a graph in last 7 days in which you can see 9 peaks between 10 and 12s and and 5 peaks at around …
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1. [x] group reads based on cluster (make bed files) https://github.com/biomystery/snATAC_pipeline_scanpy_based/commit/33d1d48b0f0357c8a91da4dfbc03a18ab17955ec
2. [x] call peaks on grouped reads http…