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Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
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Recent Replies
Comment: Redirection of Duplicate PMIDs
by
LauferVA
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let me know the scope and scale of the request (e.g. I need to do this for every record in Pubmed) and can help
Comment: Redirection of Duplicate PMIDs
by
dominickd
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I was able to come up with a workaround using the requests library:
import requests
pmid = 30134295
url = 'https://pubmed.ncbi…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
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Thanks for you answer! Actually I have already filtered my peak according to blacklist by bedtools. You mean it's meaningless to compare on…
Answer: Redirection of Duplicate PMIDs
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More than likely not since the database query seems to work for the redirected PMID but not the original.
$ esearch -db pubmed -query …
Comment: DYH17 Structure Prediction
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anasjamshed
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Blast showed PDB: 8J07_n9(human) as best template with 62.99%.
I also used swissmodel to model the protein and it showed:
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Comment: How to slice a gvcf file with tabix?
by
Sd
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Then what is the best way to do slicing for 1Mb windows? Doing `--intervals` in the GenomicsDBImport?
Comment: How to slice a gvcf file with tabix?
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> What is your suggestion to run GenomicsDBImport efficiently?
call the GVCF by slices eg: chr1:1000000-2000000<br>
run GenomicsDBImport …
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I want to run gatk `GenomicsDBImport` tool to build a GenomicsDB. I want to slice it to reduce the computation time since I have 1300 gvcf …
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The first step has to be taken outside of PLINK here. E.g. append "_1" and "_2" to the duplicated IDs in the .ped or .fam file, then menti…
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Show us the exact call to `cnetplot()` with a sample of all input parameters. Did you compare notes with your friend?
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why would you need to slice a gvcf file ? all the tools in gatk can use a BED / interval / chromosome to narrow the analysis
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Farhad
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I check dataframe it has more than 2 columns
Comment: Error in cnetplot enrichplot package
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Farhad
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We write it to csv and then send it via email
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