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Comment: Keep values from VCF file into Ensembl VEP annotation
by
dare_devil
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1.4k
it would be great and helpful to others if you share your answer here.
Answer: Expression of gene of interest across conditions in single-cell data
by
jared.andrews07
9.1k
Take a look at [dittoSeq](http://www.bioconductor.org/packages/release/bioc/vignettes/dittoSeq/inst/doc/dittoSeq.html) for viz options - it…
Comment: Extracting only tumor samples from Single cell RNASeq
by
jared.andrews07
9.1k
You need pre-defined variants for Vartrix. Typically it's used in conjuction with WGS/WES from bulk tissue to look for clonal variants in d…
Comment: Cell composition in each condition of single cell data
by
paria.alipour
▴
20
Oh, I'm sorry. I already posted it in here the https://www.biostars.org/p/457243/#9464486. I've added the images
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
•
0
This seems OK when one gene generates only one transcirpt. But when one gene has multiple transcripts, these code would return a table wher…
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
•
0
This seems feasible. But I want to convert tens of thousands of transcript IDs. Could you tell me how can I make it through sequene search?
Answer: bbmap, mapq and uniquelly mapped reads filtering
by
GenoMax
99k
Many threads exist that show how to extract uniquely mapped reads. Here are a couple of examples:<br>
https://www.biostars.org/p/276216/#27…
Comment: Cell composition in each condition of single cell data
by
rpolicastro
5.1k
The images seem to be missing from your post
Comment: Limma experiment design and making contrasts
by
kra277
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Thank you very much for this. Much appreciated.
Comment: Limma experiment design and making contrasts
by
Kevin Blighe
72k
Hi, these follow the same principles as formulae used in regression modelling, so, you may want to focus on that (when searching). What lim…
Comment: Limma experiment design and making contrasts
by
kra277
•
0
That is very insightful. Thank you very much for the answer. Also, if I may ask, could you please point me to the articles for understandin…
Comment: Keep values from VCF file into Ensembl VEP annotation
by
brunobsouzaa
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520
Thanks Man... I've wroten a simple awk command for this task! Everything is working fine.
Comment: Raw read processing using trimmomatic
by
boczniak767
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740
Do you have exact command used by the author? I guess that not all details was presented in the paper. You can always ask the corresponding…
Comment: should stop codon be counted as part of CDS
by
sullis02
•
0
Your github page appears to live here now
https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gxf.md
Comment: How do I compare degree and betweenness centrality for different PPI networks?
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Istvan Albert
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I am not all that knowledgeable of Cytoscapes features and scripting capabilities,
but if it does not support that operation you can expo…
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