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My group is currently using DropEst to process some single-cell data from erythroid differentiation, so two of our key marker genes are alpha and beta globin. Both genes are present in two identical, …
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Hi,
Lovely package for visualising the differentially expressed genes. I was trying to use it. Should the input be only DESeq2 output? How can I use it for edgeR output?
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We should think about loading the deleted genes with the `is_obsolete` flag to true. A lot of downstream code will need to change to check the flag so that obsolete genes aren't included in the query…
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@alexdobin A STAR count reported "zero" if two genes are very close sequences. Recently, I ran an experiment and found 68 genes that have zero count. I did similar count using another package in R, th…
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Thanks for sharing exciting research and the repo!
I have one question on the implementation of NS. Here, you take topk with largest=True. I believe that "largest" should be False, because you sho…
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Hello, I am trying to extract COI genes from raw Illumina sequences of cestodes to try and ID the hosts. I am using the cestodes as a proof of concept but would eventually like to try it with whole ge…
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Hi,
I was interested in getting your tutorial to work, but ran into some issues. When I ran the code on you github repo:
```python
import numpy as np
import scanpy as sc
import scdemon as sm
…
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Hi,
Thank you for this brilliant package. Using the PISCES method, I had generated 7 cell-type specific networks which I have then projected onto my single cell dataset to calculate the activity fo…
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genes.tsv from https://www.pharmgkb.org/downloads raise a stackOverflow outOfMemory error issue when running r2rml after AutoR2RML. Even if the genes.tsv files is only a couple Mo
What have been tr…
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I've run into the following error for a handful of genes:
```
/Users/albaness/miniconda3/envs/py27/lib/python2.7/site-packages/flask/exthook.py:71: ExtDeprecationWarning: Importing flask.ext.sqla…