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@enriquea I have created a simple script https://github.com/bigbio/PepBedR/blob/master/scripts/pepbedDescription.Rmd This should take a bed file as input and generate a PDF with the report of the data…
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I have downloaded the preferred assembly of 5rfa from here: https://www.ebi.ac.uk/pdbe/static/entry/download/5rfa-assembly-1.cif.gz, unzipped it and ran Arpeggio like so: `pdbe-arpeggio 5rfa-assembly-…
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GH repo: https://github.com/awgg-lab/australasiangenomes/
GH pages site: https://awgg-lab.github.io/australasiangenomes/
>Genomic data repository for the Threatened Species Initiative and the ARC…
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@sacdallago and @konstin When embedding ~500 small peptide sequences UniRep keeps taking up progressively more and more virtual memory which can cause my machine to crash.
Here is a colab notebook…
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This filter needs a certain level of flexibility for optimisation and visualizaiton - I like the FDR, miscleavage, errors of precursor mass distribution plots for the individual mzid files.
To have t…
Sjan1 updated
5 years ago
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Hello, I am having an issue using deephlapan.
I used the docker installation on MacOS. When I run the program on a test peptide or a file of several peptides, it stop at the same step.
First, I get…
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I was trying to get the longest isoform from ensemble genomesbut the function is exiting with an error
Error: Gene_ID or Peptide_IDs between the gtf file and the headers of the fasta file did not m…
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There are a few failure modes:
1) the chemical is something without a structure... should probably bring in all the identifiers a la the mesh update and chebi
2) There is a inchi, but it isn't in un…
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```
What steps will reproduce the problem?
1. import of Feature data.csv (or peptide mesarurements from Reviex protein
page)
2.export top 3 quantiatation data
What is the expected output? What do y…
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http://www.ncbi.nlm.nih.gov/pubmed/24200586