User: b.nota

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b.nota3.9k
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Posts by b.nota

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Answer: A: Pathway enrichment with differential expression p-values
... There is a nice review in [Plos Comp][1] about the different methods that are available for pathway of GO analysis. The methods (with only a list of significant genes) you are referring to are first generation. There are also second and even third generation. Read it in the paper, and you'll know wh ...
written 1 day ago by b.nota3.9k
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Comment: C: Blast of Blat for multiple sequence alignment to get each respective sequence lo
... Check [here][1] for the difference between blast and blat, and see what suits your data. I would use (stand alone) blast in this case. [1]: http://www.ensembl.org/Help/Faq?id=429 ...
written 1 day ago by b.nota3.9k
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Answer: A: duplicate 'row.names' are not allowed
... The question is also duplicate https://www.biostars.org/p/62988/ ...
written 3 days ago by b.nota3.9k
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Comment: C: how to evaluate a gene signature is present in each patient of a dataset
... Are you sure such an approach will be publishable? ...
written 3 days ago by b.nota3.9k
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Answer: A: How to find common data in replicates?
... You can use `merge` with `all.x=F` and `all.y=F` arguments. Something like: firstMerge <- merge(df1, df2, all.x=F, all.y=F) secondMerge <- merge(firstMerge, df3, all.x=F, all.y=F) ...
written 3 days ago by b.nota3.9k
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Comment: C: how to evaluate a gene signature is present in each patient of a dataset
... I think that sounds more feasible, the lasso selected features for e.g. KNN or other ML method. Take a training and test set into account. Survival is another option, it depends on your research question (can you divide patient with/without MYC amplification by gene expression profile, or the other ...
written 4 days ago by b.nota3.9k
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Comment: C: how to evaluate a gene signature is present in each patient of a dataset
... I am not sure if I understand your approach, did you find it somewhere in literature or came up with it yourself? It looks to me like you are mixing up two things, 1) machine learning, 2) limma roast. With machine learning, you select a set of genes (also called feature selection), and then with a ...
written 4 days ago by b.nota3.9k
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Answer: A: Large deletions in exome sequencing data
... There are more tools available, I tried a few and had a good experience with R (CRAN) package [ExomeDepth][1]. [1]: https://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf ...
written 4 days ago by b.nota3.9k
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Answer: A: use Homer to annotation region of ChIP-seq peaks.
... You only need the bed file produced by macs2 for homer. They need to contain the coordinates of the peaks (chr, start, end position), followed by the peak name (which is given by macs2). The output will indeed only contain "+" for each peak. ...
written 4 days ago by b.nota3.9k
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Answer: C: BWA (mem, sampe, or aln) used in bam file
... It should be in the same line following `CL:`, right after the `VN:` (which is the version of bwa). The info is thus not in your files. Here an example of a file I used: samtools view -H SRR1291026.bwa.bam | grep "bwa" @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem -t 20 /home/ ...
written 5 days ago by b.nota3.9k

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Scholar 1 day ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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