Newest Questions
6,620 questions
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Can symmetry derived waveforms be used to model physiologically plausible ECG traces and their variance? [closed]
A 2024 pre print (doi.org/10.1101/2024.10.18.619135) claims to derive a textbook-quality ECG using only the multiplication tables of point groups of order ≤ 10 and a handful of Gaussian envelopes. No ...
- 11
3
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1
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26
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Java error binding to /0.0.0.0:8080
Cytoscape 3.10.4 on Win11 crashes shortly after showing "Cytoscape Task" dialog. Running script cytoscape.bat shows error to be binding to /0.0.0.0:8080. 8080 is a port in use by another ...
- 31
3
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1
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61
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Passing .bed files to nQuire create command
I'm trying to use the nQuire create command to assess the ploidy of an individual. Specifically, I'm trying to include a .bed file along with the .bam file, in order to assess ploidy for different ...
- 165
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SNPs filtering by stacks/dDocent
I am currently doing GWAS research, and I have three libraries for later be combined to a single vcf, for later used for GWAS downstream analysis.
So, my first two library, is made using ddRADseq ...
2
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PRS across three target cohorts using UK Biobank betas: use all 20 cohorts? Or just the three? How does PRS-CS handle uneven overlap?
I have individual-level genotyping for >20 cohorts from a multi-cohort project. For a focused sub-study, I plan to compute polygenic risk scores (PRS) in three target cohorts and then use the PRS ...
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1
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1
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How can I improve ROC-AUC beyond 0.76 in predicting REST binding sites?
I'm working on a machine learning model to predict the binding of the transcription factor REST to candidate DNA binding sites for my final project in a bio-informatics course (McGill U, COMP561, ...
2
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Negative Results in McDonald–Kreitman MK test results
I’m running McDonald–Kreitman (MK) tests across several thousand genes to estimate alpha (the proportion of adaptive substitutions).
After filtering out genes with zero values for Dn, Ds, Pn, or Ps, I ...
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question about relative position encoding of alphafold3
I'm a bit confused about the specific calculation method for alphafold3's relative position encoding, because it seems that the result should be a constant.
the token-level relative position encoding:
...
- 31
4
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1
answer
104
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Nextflow error: “Invalid method invocation call with arguments (java.util.ArrayList)” when connecting processes via joined channels
I’m building a ChIP-Seq pipeline in Nextflow, and I’m running into this persistent error when trying to connect two processes that utilize HOMER's makeTagDirectory and findPeaks utilities.
The error ...
- 43
2
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1
answer
61
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RNA-seq for abundance estimation
We would like to use bulk RNA-seq for characterizing cell lines. The approach is not the "classical" differential abundance analysis where a set of samples are compared to another set of ...
- 4,242
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1
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50
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Unable to install StringApp
What is the recommended way to install StringApp? I'm using Cytoscape 3.10.4 on an Apple Silicon Mac and can download the JAR file from the App Store but opening it gives me the message:
"macOS ...
4
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16
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Duplicate regions in sample cnvkit
I am trying to run cnvkit in the following steps, for context I have tumor only samples from WES dataset:
...
- 205
2
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1
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24
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Looking for suggestions on tRNA 2D structure visualization tools (MacOS)
I’ve successfully obtained the tRNA molecule data in dot-bracket format, and I’m looking for tools that can help visualize their 2D structures.
Could anyone recommend reliable software or online tools ...
- 23
2
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1
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40
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Looking for a tool to identify all transmembrane proteins in a proteome
I am looking for a tool that identifies all the proteins of a given proteome that are predicted to have at least one transmembrane region. My proteome of interest is available in UniProt, NCBI, ...
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Discrepancies in Docking pose visualization
I’m analyzing the results of a molecular docking study performed with TomoDock, which uses AutoDock Vina.
For the ligand–protein interaction analysis, I’ve been using PyMOL, Discovery Studio ...
