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[[IndexError('index 0 is out of bounds for axis 0 with size 0'), Pandas(Index=11, ID=11, Symbol='373220')], [TypeError('cannot unpack non-iterable NoneType object'), Pandas(Index=64, ID=64, Symbol='03…
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Historically, we have focused on performance for Cray networks with comm=ugni where our intention was to ensure we have the right language features/semantics first and then expand capabilities to othe…
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Getting the above error when running MoDisco.
Minimal example to reproduce the error:
```
import modisco
import numpy as np
import tensorflow as tf
one_hot = tf.one_hot(np.random.randint(lo…
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Hi John,
Hello again. I wonder which threshold of q values do you recommend in the commend line? I tried to not set q value, set q value as 1, set q value as 0.05, respectively in my command. Here is…
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Hi dear,
I have my count matrix (featureCounts output - raw counts) with the first column as ```gene_names``` and the other two columns as ```ctrl1``` and ```kd1```. For using Clipper I generated …
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Hi, I was able to execute the Mac GUI version of this tool but running the .jar file on Ubuntu causes an error [see below]:
I have a few more questions about G2P and would be very thankful if y…
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As the title says. I will to find a way to infer proteins only when they have 2 unique peptides observed in each sample. I want to do it in Fragpipe itself. These command line options are not referenc…
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Hello,
I was wandering what are the criterias for the call made for the validation column in the PSM report file. What is considered for this?
My guess is search engine algorithm evalue associa…
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For reasons I'm not going to go into I'm not using R that comes with the conda installation of cnvkit.
For my own R installation I have my R packages in a location that's indicated in ~/.Rprofile,…
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Hi, thanks for a great package!
I am having some issues when trying to perform runHomer for motif discovery across my clusters.
Here is the code I ran
motifs = runHomer(
CD8.sp[,idy.ls…