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Recent Replies
Answer: Differential binding analysis between different TFs
by
Ming Tommy Tang
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have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/
also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session
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Dunois
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Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
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Dunois
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You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
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Dunois
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Expand your search by searching these (two) sequences against other sets of sequences.
That said, why does it feel like this is an [XY pro…
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
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It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
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I'm wondering if this could work:
`bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l`
…
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You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
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What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf
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vaellis
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I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
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example vcf:
```
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4
chr1 100 . C …
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Not totally sure I'm right about your use case (are those config entries lists of strings, which is why you need to zip them?) but, you can…
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In general, you should threshold on the p value that corresponds to the maximum FDR you can accept.
In practice, for scRNA-seq data, many g…
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I guess reference-based annotation is not an option?
In my experience, visualising the expression of canonical markers (I don't know if CD4…
Comment: count number of polymorphic sites among samples in vcf
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Ram
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I'm not sure if this will work, but you could use `bcftools view` with [include expressions](https://samtools.github.io/bcftools/bcftools.h…
Comment: count number of polymorphic sites among samples in vcf
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> However, I want to exclude sites where all of the individuals have a single alternative allele (or a mix of either one alternative allele…
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