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hello,
When running the default model and the model using purified genomic dna (default and --model msCentipede_flexbg) the tool throws 2 different errors during the learning phase of the footprint ca…
ghost updated
8 years ago
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Hi I was testing your tool on a sample and wanted to check the copy number in a specific region.
if I understood correctly the MC tag in the info field corresponds to the copy number of the motif in…
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Is it applicable for two samples to calculate the variability in normal ATAC-Seq but not single cell sequence?
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### Discussed in https://github.com/GreenleafLab/ArchR/discussions/1319
Originally posted by **wuv21** March 3, 2022
Hi!
Been running into an issue similar to #562 and #483 with the same e…
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Hi,
I am trying to compute the Cistarget step of pyscenic after obtaining meta cells with the metacell2 pipeline and then the GRN with arboreta package and saved in a tsv file. However, I keep obtain…
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Hi @AvantiShri
```
Computed threshold 2.1903742329729723
378 coords remaining after thresholding
After resolving overlaps, got 378 seqlets
1 activity patterns with support >= 200 out of 3 possib…
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maelstrom throws
```
ConvergenceWarning: Liblinear failed to converge, increase the number of iterations.
```
Possible sources:
- The warning likely originates from `LinearSVR`.
https://gith…
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Hello,
I am analyzing some RNA samples and I have noticed an issue with the quantification part using Star.
The data I have was generated by an external company using TruSeq3-PE-2 library, which…
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With the exception of added redundancies and computational time for motif_ix, is there anything wrong with doing this?
```
library(BSgenome.Hsapiens.UCSC.hg18)
library(chromVARmotifs)
library(TFB…
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**Describe the bug**
In order to perform differential enrichment, I wanted to try on a single gene, but gimme crashes.
**To Reproduce**
Steps to reproduce the behavior:
```
gimme maelstrom -N12…