Moderator: Friederike

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Friederike2.5k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

<prev • 293 results • page 1 of 30 • next >
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Comment: C: Removing duplicated mutations from a txt
... If you read in the file as a `data.frame` or `data.table` into R (!), you can use `unique(my_dataframe)`, no need to sort, if I recall correctly (but it may take some time). Which function of R returns the error message; it's somewhat difficult to believe it's related to the sorting and uniq'ing th ...
written 46 minutes ago by Friederike2.5k
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Comment: C: Cuffdiff in highly different samples
... > In theory Cuffdiff should call as upregulated all the genes in the sample (b). This of course did not happen How do you know that's true? However, I'm not sure I totally follow -- are you saying, you're detecting different numbers of genes in the different data sets? How can "all genes in d ...
written 1 hour ago by Friederike2.5k
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Comment: C: How to compare samples between two different platforms?
... If you are missing genes in one assay, you can hardly compare its expression values between the two methods. Unless you had another way of calculating the correlation in mind, my answer would be: yes, absolutely do you need to look at the same genes in both assays. ...
written 3 days ago by Friederike2.5k
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Comment: C: How to compare samples between two different platforms?
... Yes, if you have 50 samples, you want to calculate all their pairwise comparisons to each other. Maybe the [corrplot package](https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html) is helpful here. Which RNA-seq values did you use for the clustering of the RNA-seq data? I w ...
written 3 days ago by Friederike2.5k
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Answer: A: Gene list of Neuronal Markers for TSNE plot
... Welcome to the cumbersome and surprisingly ambiguous world of "identifying cell types" from scRNA-seq data! Both of the answers are helpful, the first thing that came to my mind was [The Allen Brain Atlas](http://celltypes.brain-map.org/download#transcriptomics) -- but the more you ask, the more ma ...
written 4 days ago by Friederike2.5k
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Comment: C: What kind of R Project I can do related to gene expression analysis or protein c
... If you want to skip the first command-line-based steps, you could start from the read counts using the `recount` package and [their workflow](https://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html#4_sample_de_analysis) EDIT: Some background info -- both, G ...
written 6 days ago by Friederike2.5k
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Comment: C: Reproducing this picture
... The VCF file that you used for VEP should have that information ...
written 10 days ago by Friederike2.5k
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Answer: C: Reproducing this picture
... Did you check the help for `waterfall` or `lolliplot`? I haven't used those packages, but it seems to me you will need the genomic coordinates of both the gene as well as the mutations. You will likely have to do some data wrangling to parse the location of the mutation of the file you linked into t ...
written 11 days ago by Friederike2.5k
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Comment: C: Which NGS aligner to find inexact matches
... > BWA MEM reporting not just PERFECT matches, but other matches with < 100% identity and < 100% query sequence coverage Yes. BWA-MEM has myriad parameters which you can tune, including how many mismatches you allow. ...
written 11 days ago by Friederike2.5k
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Comment: C: ChIP-Seq density plot of the TSS regions?
... > I know how to use deeptools but I don't think its giving results as I want How is that? I.e. what type of result to you get and what do you not like about it? ...
written 11 days ago by Friederike2.5k

Latest awards to Friederike

Scholar 4 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 20 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 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 4 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 5 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Good Answer 10 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?
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
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 4 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 4 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
Epic Question 4 months ago, created a question with more than 10,000 views. For Understanding ATAC-seq data
Appreciated 5 months ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
Good Answer 5 months 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 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
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
Appreciated 5 months ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
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
Good Answer 6 months 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?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
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
Scholar 6 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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
Good Answer 6 months 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?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Why do peak shifts occur?

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