User: Friederike

gravatar for Friederike
Friederike840
Reputation:
840
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Location:
United States
Last seen:
2 days, 10 hours ago
Joined:
2 years, 9 months ago
Email:
m**********@immunbio.mpg.de

Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

http://abc.med.cornell.edu/

Posts by Friederike

<prev • 88 results • page 1 of 9 • next >
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Comment: C: Semantic Similarity selection in REVIGO: which is better?
... I would say it depends on the question you want to address. ...
written 2 days ago by Friederike840
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Comment: C: Semantic Similarity selection in REVIGO: which is better?
... this comment of yours: >is it a good Idea to put and show the case and control in one TreeMap or we should show them in two separate TreeMaps makes me want to know what your actual input to REVIGO is. I was under the impression that the typical use case would be: DE analysis --> enriched GO ...
written 2 days ago by Friederike840
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Comment: C: Inconsistent Coverage on X chromosome between genders
... Based on the replies here I guess I am not the only one who doesn't fully understand the issue at hand. Can you clarify what your expectations are for both, on-target and off-target, and why? ...
written 2 days ago by Friederike840
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Answer: A: how to display multiple row annotations on pheatmap
... from the pheatmap help: ``` # make test matrix test = matrix(rnorm(200), 20, 10) test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3 test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2 test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4 colnames(test) = paste("Test", 1:10, sep ...
written 2 days ago by Friederike840
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Comment: C: Apply Deseq2 size factor to aligned reads
... If you want to be totally clean about that, you could remove those reads from the BAM file that are not being taken into consideration for the read count matrix. Not sure if featureCounts can tell you the read IDs that it's using, but since it comes with an aligner, maybe there is a way to retrieve ...
written 2 days ago by Friederike840
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Comment: C: single cell RNA-seq detected genes
... Hi Mike, I have not seen such a pattern, but I've also never directly dealt with raw data from SMART-seq experiments, so I cannot comment on whether that's something that is often seen. I also don't have much experience with kallisto yet, but given that it's a transcript quantifier that may be inf ...
written 8 days ago by Friederike840
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Comment: C: Bulk RNA-Seq data analysis
... the analyses you're going to do should ideally be guided by biological questions. what were the reasons to generate that data? ...
written 9 days ago by Friederike840
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Comment: C: single cell RNA-seq detected genes
... can you share the plot? and can you check the most strongly expressed genes per cell? my first guess would be that many reads might be scavenged by ribosomal or other highly abundant transcripts, thereby reducing the diversity of transcripts despite an increased sequencing depth, but it would indee ...
written 9 days ago by Friederike840
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Comment: C: Strange distribution of logFC
... I'm also missing the problem here -- it's quite normal to see changes in both directions, i.e. up- as well as down-regulated genes. Is there a reason why you expect only changes into one direction? ...
written 10 days ago by Friederike840
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Comment: C: How to associate a row from one data frame with a value in another data frame ba
... seeing all these diverse answers rolling in it'd be great if you could benchmark them on your large data set! ...
written 15 days ago by Friederike840

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