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Answer: 'SyntaxError': 'return' outside function?
Comment: Analyzing bulk RNA-seq
The Biostar Handbook. A bioinformatics e-book for beginners.
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lncRNA analysis tutorial
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
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Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
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If this is the case then you cannot correct for anything as this effect is nested with center.
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That error message is very descriptive. Could you also add the line 997531?
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Thanks for the answer. However I am not sure this could be considered batch since CC2 samples have true upregulation of specific pathways t…
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dr.fakharunnisa
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Hello #gubrins Have you found the answer
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The `object` will the the Seurat object you're working with, because that contains the data that will be plotted (Tn5 insertion events per …
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Using [**Entrezdirect**][1]. Date in last column is collection date. No way to query using it though. Could be wrong. $ esearch -db nu…
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Pretty sure that nothing other than HHsuite outputs results in `.hhr` format.
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Same allele = weight of 1, different allele = weight of 0. You can read more here: https://choishingwan.github.io/PRS-Tutorial/plink/#gener…
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Hi jv, Thank you for your help. But I am still uncertain. The GSEA tools can process the preranked list. However, it still required that I…
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
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Jiyao Wang
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You can also try out [iCn3D](https://structure.ncbi.nlm.nih.gov/icn3d). After you load your custom PDB via the menu "File > Open File > PDB…
Comment: CoveragePlot in Signac from MACS2 Object
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What is 'peaks' entered as?... The input is: CoveragePlot( object = pbmc, region = "CD8A", ranges = peaks, …
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Nick
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I totally get your point, maybe long-winded was also not the right description for my issue. One example, [custom databases][1] are very cl…
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Wouldn't you take your MACS2 files, import them with rtracklayer so that they are GRanges objects, and then pass those as the peaks? i.e. w…
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Honestly, I think most RNASeq aligners are fairly robust to adapters. You could probably get away with not trimming at all
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