Moderator: Friederike

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Friederike6.7k
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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: How to get geneIDs from XLOCs?
... Disclaimer: I have never used CuffDiff. What does `featureNames(diffGenes)` get you? Can you supply the result of `head(featureNames(diffGenes))`? Btw, I strongly recommend to NOT assign the output to an object named "names" as that is the name of a base R function (type `?names`) ...
written 9 days ago by Friederike6.7k
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Comment: C: Seurat to Dataframe with ONLY counts, cells, and cluster labels?
... what does `data_transcripts_seurat@active.ident` get you? Shouldn't those be the cluster assignments per cell? [Disclaimer: I do not use Seurat, so I'm basing this off your initial code] ...
written 9 days ago by Friederike6.7k
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Comment: C: Loop function for ggplot2 bar chart for multiple variants
... instead of `aes(x = treatment, y = mean, fill = treatment)` do `aes(x = time, y = mean, fill = treatment)` or `aes(x = treatment, y = mean, fill = time)` ...
written 10 days ago by Friederike6.7k
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Comment: C: How to get geneIDs from XLOCs?
... >it did not work for me What exactly did you try? ...
written 10 days ago by Friederike6.7k
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Comment: C: Can I use different library-prep methods for one RNAseq experiment?
... Absolutely try to go with just one method. The library prep step is one of the key steps that has been shown over and over again to introduce significant bias depending on the method, and no bioinformatics magic will be able to completely rescue that. If one method is not feasible, the only way to ...
written 10 days ago by Friederike6.7k
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Comment: C: Collapsing my paired-end reads before or after mapping ?
... This would be the point where you could dig into the documentation of EAGER to find out how the collapsing is done. Presumably they are leveraging the fact that both reads tend to cover the same piece of a fragment. ...
written 10 days ago by Friederike6.7k
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Comment: C: Seurat to Dataframe with ONLY counts, cells, and cluster labels?
... Why not start with `data_transcripts_seurat@assays$SCT@counts`? Something like: ``` counts.df <- as.data.frame(data_transcripts_seurat@assays$SCT@counts) ``` If you need the cells to be rows, you can use the `t()` function: ``` counts.df <- data_transcripts_seurat@assays$SCT@counts %>% ...
written 10 days ago by Friederike6.7k
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Comment: C: Loop function for ggplot2 bar chart for multiple variants
... good catch, will update ...
written 11 days ago by Friederike6.7k
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Answer: C: Loop function for ggplot2 bar chart for multiple variants
... If you set up the table correctly you don't even need a for-loop. Your table should look like this (the order of the columns does not matter): ``` treatment time Protein mean sd 1 group1 24h A 1 0.15 2 group2 24h B 10 1.10 ``` Then you can do: ``` ggplot( ...
written 11 days ago by Friederike6.7k
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Comment: C: which tool should be used to call the genotype?
... mutect and haplotypecaller are tools for identifying reference and alternative alleles, yes. Your question is lacking context (e.g. did you sequence a single gene or entire genomes? how many samples do you have? what is the ultimate goal of the analysis? have you tried (and possibly failed) specif ...
written 11 days ago by Friederike6.7k

Latest awards to Friederike

Good Answer 9 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?
Student 16 days ago, asked a question with at least 3 up-votes. For Understanding ATAC-seq data
Scholar 27 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Understanding ATAC-seq data
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 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 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
Scholar 12 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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?
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
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
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?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Popular Question 7 months ago, created a question with more than 1,000 views. For Understanding ATAC-seq data
Teacher 8 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 8 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Scholar 8 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 9 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 9 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 9 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells

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