User: Friederike

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Friederike2.0k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

<prev • 241 results • page 1 of 25 • next >
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Comment: C: Why do peak shifts occur?
... only if you seek to find binding sites of proteins on transcripts using antibody-based enrichment of your factor of interest as it is binding to RNA. generally, it would be imprecise say that the reads are shifting -- the reads are always going to represent the **ends of the (c)DNA fragments** that ...
written 6 hours ago by Friederike2.0k
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Comment: C: how to display multiple row annotations on pheatmap
... you can use the continuous annotations as is, pheatmap will take care of it ...
written 7 hours ago by Friederike2.0k
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Answer: A: What is the difference between Bioconda and Galaxy?
... Bioconda is a package manager that makes the installation of your tool easier. Most likely, this will be used by bioinformaticians that do their own analyses and installations (of command line tools). That means, the person installing and using the tool will most likely be the same. Galaxy is a web ...
written 2 days ago by Friederike2.0k
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Answer: A: is Amazon Web Services (AWS) useful?
... Have you looked into [DNAnexus][1]? That's a cloud-based service geared towards bioinformatics; they basically try to act as an intermediary between the basic cloud infrastructure and specific bioinformatics needs. They provide numerous pre-installed tools, for example, and also have a couple of pip ...
written 2 days ago by Friederike2.0k
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Answer: A: why do bed files not contain information about the reference?
... Because of the eternal fight between simplicity and full documentation. BED files are super simple and basic. Yes, you can add a comment in the beginning (or you could just make a note of the genome version in the file name). Or you can use the infinitely [more complex R objects for storing genomic ...
written 7 days ago by Friederike2.0k
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Comment: C: Why survival plots look different with same data?
... you have one sample less (247 instead of 248 for one group). Also: did you remove everything FPKM < 1? ...
written 9 days ago by Friederike2.0k
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Answer: A: Why survival plots look different with same data?
... I have nothing of substance to contribute except that the actual details of the analysis matter since the Human Protein Atlas people themselves show that the same data can very well yield differently looking survival plots: [https://www.proteinatlas.org/ENSG00000119927-GPAM/pathology/tissue/liver+ca ...
written 9 days ago by Friederike2.0k
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Comment: C: Extract only rows with main chromosomes (1-22, X, Y) on first column?
... yes, you're right, the dollar sign in the original command I posted was silly (only makes sense for the R-based command) ...
written 9 days ago by Friederike2.0k
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Answer: C: extract only rows eith numbers?
... command line: ``` egrep "^[0-9XY]" file ``` EDIT: originally, this used the same regex as for the R-based example (`^[0-9XY]$`). This won't work because the full line of the text file contains more characters (such as the coordinates...). Thanks to Alex for pointing this out. R (because this post ...
written 10 days ago by Friederike2.0k
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Comment: C: R Syntax Question, Bioconductor data
... you're welcome. good luck with your analyses! ...
written 20 days ago by Friederike2.0k

Latest awards to Friederike

Appreciated 1 day ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Scholar 10 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Appreciated 20 days ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Scholar 20 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Scholar 3 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Great Question 9 months ago, created a question with more than 5,000 views. For Understanding ATAC-seq data
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