User: Friederike

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Friederike2.3k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

<prev • 277 results • page 1 of 28 • next >
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Answer: A: RNA-seq analysis using R
... Generally, most people will do the very first steps, i.e. QC and alignment of the raw reads stored within the FASTQ files, outside of R, e.g. using STAR or Salmon/Kallisto as described in this [workflow by Mike Love][1]. If you want to do the alignment using an R package, you may want to give the [R ...
written 14 days ago by Friederike2.3k
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Answer: C: Explore objects in R (ChiPseeker)
... Does `table(peakAnnoList[[1]]@detailGenomicAnnotation$genic)` get you what you want? I think part of the issue here is that we don't really have the object you're dealing with, so it's a little tricky to give you the precise code. You'll have to do some fiddling apparently or go back to the document ...
written 15 days ago by Friederike2.3k
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Comment: C: Explore objects in R (ChiPseeker)
... so that means you could, for example, use the command above for that list object: ``` x <- as.data.frame(peakAnnoList[[1]]) ``` ...
written 16 days ago by Friederike2.3k
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Comment: C: Explore objects in R (ChiPseeker)
... This probably means that it is a `list` of these objects, so `lapply(peakAnnoList, as.data.frame, head)` might be worth a try. If you want more concrete help, you should update your question to include the result of `str(peakAnnoList)` and what exactly it is you're trying to do/to see. ...
written 16 days ago by Friederike2.3k
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Comment: C: Handling biological replicates across batches in DESeq2
... > individual samples are correlated to each other that might not be accounted for in the design Not sure what you mean by this. Michael Love has explained the issue quite well. Either your technical replicates are very similar to each other --> in this case, merge them. I would probably do ...
written 6 weeks ago by Friederike2.3k
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Comment: C: Handling biological replicates across batches in DESeq2
... `~Genotype + Sex + Condition` should allow you to query all of the contrasts you mentioned were of interest to you, i.e. ``` > sample_info DataFrame with 10 rows and 3 columns condition sex genotype SNF2_1 SNF2 male Het SNF2_2 SNF2 ...
written 6 weeks ago by Friederike2.3k
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Comment: C: Handling biological replicates across batches in DESeq2
... I did not suggest to combine Sex, Condition, Genotype. I suggested to collapse Batch & Sample. ...
written 6 weeks ago by Friederike2.3k
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Answer: C: Handling biological replicates across batches in DESeq2
... If I read your description correctly, you have a set of samples for which you have 2 batches and another set of samples for which you have only 1 batch? I'd drop "batch" from the picture, similar to what you tried with `SequencingBatch_Sample`, i.e. combine the info about batch and sample into one n ...
written 6 weeks ago by Friederike2.3k
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Comment: C: Bedtools intersect alternatives available
... is there a difference in how bedtools and bedops interpret the intervals? (i.e., zero-based half open vs. 1-based etc.) ...
written 7 weeks ago by Friederike2.3k
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Comment: C: Plot of 2 replicates
... Can you share the code (including the `gather` command) and plot that you generated and that you want to optimize? ...
written 8 weeks ago by Friederike2.3k

Latest awards to Friederike

Appreciated 21 days ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
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 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
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
Epic Question 11 weeks ago, created a question with more than 10,000 views. For Understanding ATAC-seq data
Good Answer 12 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 12 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
Appreciated 3 months ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
Appreciated 3 months 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
Good Answer 3 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 3 months ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
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
Scholar 4 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Appreciated 4 months ago, created a post with more than 5 votes. For A: Why do peak shifts occur?
Good Answer 4 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 4 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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
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 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
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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