Moderator: Friederike

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Friederike4.3k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

<prev • 504 results • page 1 of 51 • next >
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Comment: C: DESeq2 pheatmap by genefilter in R
... my first guess would be that the error is due to **lack of row.names** for the `anno` object. `annotation_col` expects a data.frame, where the content defines the groups of interest (e.g. the condition), and the row.names correspond to the individual sample names (i.e. the colnames of your matrix). ...
written 3 minutes ago by Friederike4.3k
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Comment: C: DESeq2 pheatmap by genefilter in R
... Please add the results of `head(mat)`, `str(mat)`, `head(anno), `str(anno)`. ...
written 4 hours ago by Friederike4.3k
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Comment: C: bed graph and IGV
... nothing to be ashamed of, typos/omissions are the bane of every coder's existence ...
written 3 days ago by Friederike4.3k
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Comment: C: Can we combine adjacent peaks in ATAC-Seq fata
... In concur with Chirag plus I will say that drawing conclusions on how to treat *all* peaks based on a single observation is probably not the most robust way forward. ...
written 3 days ago by Friederike4.3k
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Answer: A: Can we combine adjacent peaks in ATAC-Seq fata
... Peak calling software, such as MACS2 or [HMMRATAC](https://github.com/LiuLabUB/HMMRATAC) or [Genrich](https://github.com/jsh58/Genrich#pcr-duplicate-removal) have been developed to identify regions of enrichment and assign statistical metrics to their results. You can choose to believe their assignm ...
written 3 days ago by Friederike4.3k
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Comment: C: How to scale data between two different platforms: RNA Seq and Illumina
... Yes, quantile normalization, for example. But the question is whether the results will be meaningful at all because RNA-seq and microarrays return very different types of measurements (RNA-seq: integer counts of DNA fragments; microarrays: fluorescent intensities), which is why Asaf is pointing out ...
written 5 days ago by Friederike4.3k
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Comment: C: Barplot with base point as 0.5
... There may not be a more direct solution because the creator of ggplot does have some opinions about how plots and particularly axes should look like. In any case, I would recommend you post that question in a forum dedicated to R since this is not a problem specific to bioinformatics (which is the f ...
written 5 days ago by Friederike4.3k
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Comment: C: How to scale data between two different platforms: RNA Seq and Illumina
... Can you clarify what you mean by "Illumina data"? Typically, most RNA-seq samples are generated on Illumina machines, too, which is why I'm not fully following. Do you mean that one set of samples was based on microarrays? ...
written 5 days ago by Friederike4.3k
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Answer: A: GO redundancy reduction
... For automating REVIGO submissions, you can use [this python script](https://gist.github.com/daler/5473540) (which I originally found on biostars, too, I believe). I don't fully remember which changes I made, but you can see my version [here](https://github.com/friedue/randomScripts/blob/master/downl ...
written 5 days ago by Friederike4.3k
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Comment: C: GO redundancy reduction
... Ah, that's a different question then! :) Why don't you re-phrase your question to something like "How can I automate REVIGO" and I'll point you to a script that does it. ...
written 5 days ago by Friederike4.3k

Latest awards to Friederike

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 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
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
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
Scholar 6 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 6 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 6 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
Good Answer 8 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?
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 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 11 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 11 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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