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This is a detailed list of notes corresponding with openjournals/joss-reviews#4913. The checklist below may be modified as the review progresses. I'll create a separate issue for any items that requir…
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I am trying to run philosopher pipeline with version 5.0, but I keep getting an error. The data consist of 12 samples and 48 fractions for each sample (label free). I get this error when I try to lau…
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if I wanted to analyze KO / KEGG pathways or COGs between MAGs from different environments, what would you recommend to do with the eggNog annotations from ATLAS? as there are many KO numbers/COGs, wh…
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I'm working through the book sequentially and these are my comments on chapter 2. I've also made some direct edits to the text for more minor things and writing adjustments and issued a [pull request]…
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Hello,
Specifically, I have an integrated Seurat object and I used the "FindMarkers" function to generate a list of differentially expressed genes between two conditions (diseased and control) of…
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Hello everyone,
I noticed in the code `erdogant/distfit/distfit.py` that whenever you use the KS statistical test (`stats=ks`), you call the `scipy.stats.ks_2samp` to test your data against the dis…
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Consider the following code:
``` Python 3
from statsmodels.distributions.empirical_distribution import ECDF
import numpy as np
ecdf = ECDF([1,2,2,2,3])
print(np.vstack((ecdf.x,ecdf.y)))
```
…
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Hi there. I'm trying to follow along with the instructions on the R vignette and am having absolutely no luck pinpointing why I can't get this to work.
I've created a path model in piecewiseSEM as …
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One of the items in the JOSS review criteria #1 is:
> **Functionality:** Have the functional claims of the software been confirmed?
Many have, but I still don't understand some things.
1. I h…
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One big question is how well this model generalizes. The expected decrease in accuracy is probably as follows, from best-performing to worst-performing:
1. MESOSCOPE data (also from the Ingalls lab…