User: Friederike

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Friederike1.3k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

<prev • 151 results • page 1 of 16 • next >
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Answer: A: Split bam files from ATAC-seq PE data into nucleosome free and nucleosomal regio
... haven't used it myself, but I remember that `ATACseqQC` did something along those lines -- check out their [vignette][1] [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html#split-reads ...
written 5 hours ago by Friederike1.3k
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Comment: C: How can I use function from xxx package in my package as member function.
... Hi Pijush, from a brief look at the repo structure everything looks like it should - anything in particular you would like to have double checked? Thumbs up for providing a vignette! You could actually check biostars whether there's already a way to a) promote your package while b) getting construc ...
written 1 day ago by Friederike1.3k
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Comment: C: How can I use function from xxx package in my package as member function.
... I think either one should work, no? i.e. either `#' @importFrom` and then one should be able to use the function without the package name pre-prended *or* `packageName::functionName()` ...
written 1 day ago by Friederike1.3k
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Comment: C: Principal component analysis (PCA)
... seconding Ram, it is particularly not clear what the question is you want to address and what the specific error might that you're encountering. ...
written 1 day ago by Friederike1.3k
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Answer: A: How can I use function from xxx package in my package as member function.
... a clean way to do is to: 1. add package `XXX` to the `Suggests:` part of `DESCRIPTION, i.e.: ``` Package: NewPackage Type: Package Title: < > ... Suggests: XXX ``` 2. use the function within your package using this notation: `XXX::the_original_function_na ...
written 1 day ago by Friederike1.3k
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Comment: C: How to concatenate two fasta files, using regular expressions
... concatenation is usually referred to when you add two lines underneath each other. from your example it seems as if you want both concatenation and pasting (= the adding of two columns next to each other) I assume that your files are labelled somewhat systematically, so pasting the sequences of th ...
written 8 days ago by Friederike1.3k
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Comment: C: Nomalize chip-seq data
... >if you are looking at a global increase or reduction of whatever you are ChIPping, total read normalization will not work. This depends on the nature of the ChIP. Transcription factor ChIP-seq often have relatively few (<20K) enriched regions, which should not influence the global scaling ap ...
written 8 days ago by Friederike1.3k
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Comment: C: Where to download blacklisted regions?
... you could use `bedtools merge -i blacklist.bed` to merge those overlapping regions. ...
written 8 days ago by Friederike1.3k
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Comment: C: Where to download blacklisted regions?
... I'm afraid I don't understand the issue. Can you elaborate? ...
written 13 days ago by Friederike1.3k
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Comment: C: ATAC-Seq High Unaligned Percentage
... amount of DNA is certainly a main contributor. I'm not a wet lab person so I don't know the specifics of how to get rid of adapters, I'd imagine there might be some way to clean the samples before you put them on the flow cell. ...
written 26 days ago by Friederike1.3k

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Teacher 5 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 8 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
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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
Great Question 5 months ago, created a question with more than 5,000 views. For Understanding ATAC-seq data
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Good Question 5 months ago, asked a question that was upvoted at least 5 times. For Understanding ATAC-seq data
Teacher 6 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 14 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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