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Recent Replies
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
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jared.andrews07
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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
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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
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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
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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
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Kevin Blighe
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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
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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
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brunobsouzaa
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Thanks Man... I've wroten a simple awk command for this task! Everything is working fine.
Comment: Raw read processing using trimmomatic
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boczniak767
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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
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sullis02
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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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Istvan Albert
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you would get the counts as you would get them in any other case, how do you know something maps to chromosome 1 of human genome? Because i…
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