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When running a similar example as issue #51, there's a mysterious error "Cannot index with multidimensional key". Running the dev branch.
```
import pandas as pd
from glycowork.motif.analysis imp…
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Hi,
I want to know what file to use in the below two steps;
TOBIAS ATACorrect --bam test_data/Bcell.bam --genome test_data/genome.fa.gz --peaks test_data/merged_peaks.bed --blacklist test_data/…
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Hi,
How can I incorporate homer pwms motif list and mouse pwms v2 list into the STREAM_scATAC-seq-motif.ipynb?
Thanks!
SH
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Hi, I have been trying to use expansion hunter denovo to
analysis some WGSs in cram format and I am getting motif/locus output files
that appear truncated. For instance both my motif and locus files…
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Similar to issue #53. When terminal 1 is combined with terminal2 a similar error happens. It seems to be specific to just this combination, I tried a few other combinations and they worked. I assume t…
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Fang Lab,
Unfortunately the singularity installation option wasn't working for for our campus cluster or my lab machines. As such, I had to set up a conda environment on our cluster and attemptted …
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Hi
First of all, thanks a lot for such a nice and useful tool!
I have two sets of ATAC-samples; control cells and cells over-expressing TF A. I have ChIP-seq peaks for TF A which are the regions t…
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This Problem Solving issue is an attempt to reach consensus about the behavior described in rakudo/rakudo#3726 and discussed further in raku/doc#4356; see also [a related StackOverflow post](https://s…
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For figure 2 in Akita how were the CTCF positions identified? In the methods section it says "To perform in silico motif mutagenesis, we intersected our test set regions with motif positions using bed…
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Organize thoughts and outlines with Lesli about data needed for the clustering algorithm. Make sure that the outlines are clear so that we can move forward to Q5 seamlessly. Provide an outline of the …