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Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: Understanding STAR output (Aligned.out.sam file)
Comment: High Malat-1 expression in single cell data
Comment: removeBatchEffect explained using base R linear models
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Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases
by
jared.andrews07
★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype
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GenoMax
142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype
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Pierre Lindenbaum
161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python
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Wayne
★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea()
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1769mkc
★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
Comment: Applying the metacell2 algorithm using python
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JACKY
▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
Comment: Repeated testing/data mining in RNA Seq
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robert.flynn.21
• 0
Thanks! I'll give it a go.
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
Yes, they are very clear about this. The page about the Vignettes says: >"They are not meant as a comprehensive documentation of all the fe…
Comment: Gene density plot
by
dthorbur
★ 1.9k
This sounds like it would be a simple task in either python or R. Read data in, potentially with a library like `data.table` in `R`, depend…
Answer: HLA-HD tool for genomic imputation
by
Javier
• 0
Hi, I just solved the same error. In my case, it was because I misunderstood the instructions. hlahd.sh -t 4 *-f ~/hlahd.1.7.0/fr…
Comment: Question regarding WGCNA
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andres.firrincieli
3.6k
Ok, then. You likely have a scale free topology that look like this: [link][1] In this situation you should pick the power value with an …
Comment: Bioinformatics Analyst - Laboratory Medicine and Pathology
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Ram
43k
Why did you add this as an answer to a random post? I'm moving this to a comment. To answer your question, read this post: https://www.bio…
Comment: ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG lin
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GenoMax
142k
> I don't understand why SAM header has "Duplicate entry" and what should I do in this case. Your reference sequence must have fasta head…
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