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Recent Replies
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴
110
Thank you for replying again. The "type" still causes issues but the reply by Radu Tanasa worked.
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
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110
Thank you so much. That worked perfectly and it was much faster than what I was trying.
Answer: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
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0
I'm still stuck on how to fix this.
Answer: How to plot proportion of cells in each cluster with scanpy?
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Hi. If I get this right, you simply need to compute the percentage of cells in each cluster at the dataset level?
```py
import pandas as p…
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Why would that be an advantage?
Comment: How to plot proportion of cells in each cluster with scanpy?
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bk11
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The following code will write percentage in your stacked barplot.
cross_tab = pd.crosstab(adata.obs['leiden_0.6'],adata.obs['typ…
Comment: How to check RNAseq support for annotated genes?
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BioinfoBee
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@juke34 Thanks for the suggestion. I wonder if bedtool coverage or intersect can be used to check the transcript support or coverage for ea…
Comment: How to plot proportion of cells in each cluster with scanpy?
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Because that was the code from the link. It is how they specified they had 2 groups of samples but I don't have 2 groups. Sorry for the con…
Comment: Violin plot (Monocle 3) - Troubleshooting
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bk11
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No there is no bug in this. Please see carefully what the `error` message tells to you.
Comment: How to check RNAseq support for annotated genes?
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@michaeld Thanks. I tried it using STAR to map the transcript to the annotation gtf file, and was planning to use featureCounts/gene Counts…
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Why you had `type` in your code above then?
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R's dplyr will serve well here.
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Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
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Thank you for the suggestion. Unfortunately, that does not work for me because I do not have a "type" argument in the adata.obs.
I think th…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
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I'm still seeing errors:
First I tried the code you mentioned except I use `clusters` instead of `embryo.time.bin` since this is a column…
Comment: Comparing multiple columns from two files using AWK
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Thank you for the formatting support. Please, can you suggest the code (R/Python) to approach my problem? Something I can use as a starting…
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