Moderator: Friederike

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Friederike6.3k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

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Comment: C: Plotting ChIP seq signals in specific regions
... Sorry, I don't get what you're envisioning. Do you have an example image you could link to? ...
written 1 hour ago by Friederike6.3k
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Answer: C: Plotting ChIP seq signals in specific regions
... You can generate the density plot and heatmaps using the peaks. If you have 2 BED files with the peaks from TF 1 and those from TF 2, you can feed those into deepTools' `computeMatrix` as described [here](https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html?highlight=computeM ...
written 3 days ago by Friederike6.3k
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Comment: C: Computational Biology Programming Course/Book
... What is your background? ...
written 3 days ago by Friederike6.3k
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Comment: C: Finding molecular divergence
... > I have no idea where to start I suggest PubMed and your favorite web search engine, e.g. using a query like "phylogenetic analysis virus tutorial" ...
written 3 days ago by Friederike6.3k
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Comment: C: increase spacing between groups in a bar plot
... you don't actually make use of the dodging because your groups are unique. What are the entries of `group` supposed to capture? You need to add a group ID that captures the sets that you want to plot as a group as shown in the blue square annotation above. EDIT: read your code more carefully, so no ...
written 4 days ago by Friederike6.3k
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Comment: C: Finding molecular divergence
... Well, what data *do* you have? ...
written 4 days ago by Friederike6.3k
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Comment: C: Could any one explain about the pairwise alignment matrix.
... If that is your question, I recommend you either close this one and post a new question or you edit your question and title accordingly so that the right people will pick it up. ...
written 4 days ago by Friederike6.3k
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Answer: A: classify contaminants in bisulfite treated whole genome data
... That is a very normal mapping efficiency value for WGBS. After all, you're mapping to a reduced alphabet (3 bases instead of 4) and you've treated the DNA rather harshly. The fact that nothing comes up in your BLAST query supports the notion that the 25% reads that couldn't be mapped are most likely ...
written 4 days ago by Friederike6.3k
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Comment: C: could any one explain about the pairwise alignment matrix. I'm struggling hard e
... Congrats, you've done step 1 "generate a 3D structure for this protein". Based on the remainder of the question, you should probably determine which tool uses Homology Modelling and which one uses Protein Threading and compare the results you obtain from either one. Unless you can come up with a s ...
written 4 days ago by Friederike6.3k
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Comment: C: could any one explain about the pairwise alignment matrix. I'm struggling hard e
... Please adjust the title accordingly ...
written 4 days ago by Friederike6.3k

Latest awards to Friederike

Teacher 3 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
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 6 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Good Answer 4 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?
Scholar 4 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 4 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 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 7 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
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?
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Popular Question 4 months ago, created a question with more than 1,000 views. For Understanding ATAC-seq data
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
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Scholar 5 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
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 7 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Student 9 months ago, asked a question with at least 3 up-votes. For Understanding ATAC-seq data
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Good Answer 9 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?
Scholar 12 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells

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