Moderator: Friederike

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Friederike3.3k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

<prev • 393 results • page 2 of 40 • next >
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Answer: A: Small dataset for data analysis in the own laptop
... I'd look for data from yeast or Drosophila. While the biases are slightly different than for mouse and human (fewer headaches with alternative splicing, different GC biases), these are widely used model organisms with tons of data sets and lots of insights to be gained -- and their genomes/transcrip ...
written 6 days ago by Friederike3.3k
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... yes, `rnames <- data[,1] ` will extract the content of the first column, not the first row. That would be achieved with `rnames <- data[1,]`. ...
written 8 days ago by Friederike3.3k
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Answer: A: How to generate KEGG pathway classification chart
... I like `clusterProfiler` for this task, it provides fairly straightforward integration of both [KEGG Pathway Enrichment Analysis](https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html#kegg-analysis) as well as [visualizations](https://bioconductor.org ...
written 8 days ago by Friederike3.3k
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Answer: A: heatmap with ggplot: problem when indicating min and max value
... If you want to assign colors to fixed min/max values, you shouldn't actually change the values you're plotting. Instead, you can use `scale_colour_gradientn` to manually define the color range, [this post](https://stackoverflow.com/questions/18487369/ggplot-set-scale-color-gradientn-manually) might ...
written 8 days ago by Friederike3.3k
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Comment: C: Microarray analysis in R (Limma): how to select genes exclusively expressed in o
... the expression for "not NA" is this: `!is.na(x)`, i.e.: `subset(tt, !is.na(a) & is.na(b) & is.na(c) )` ...
written 8 days ago by Friederike3.3k
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Comment: C: How can you merge more than two 10x datasets in Seurat?
... >when I merge the 3rd t seems like the metadata isnt saved I'm not sure I completely understand what's going on -- could you perhaps post the results of `str()` on the individual files as well as the merged files and keep the commands you run in between as well? ...
written 9 days ago by Friederike3.3k
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Answer: A: scRNA-seq python tutorial
... The [scanpy tutorials](https://scanpy.readthedocs.io/en/latest/tutorials.html) might be a good start. ...
written 9 days ago by Friederike3.3k
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Answer: A: Microarray analysis in R (Limma): how to select genes exclusively expressed in o
... I absolutely second Kevin's advice, but if you need to figure out how to subset a data.frame based on NA values, these examples may give you some leads: ``` > tt <- data.frame(a = c(NA, 1,2,3), b = c(NA, NA, 1,2), c = c(NA, NA, NA, 1)) > tt a b c 1 NA NA NA 2 1 NA NA 3 2 1 NA 4 3 ...
written 9 days ago by Friederike3.3k
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Comment: C: Data integration strategies for single cell RNA-seq
... If you want to map cells from different conditions to the same clusters, the alignment step is certainly the most elegant one. Otherwise, you should keep the pre- and post-treatment samples separate, determine the clusters and see if you know which clusters from pre correspond to which clusters in t ...
written 11 days ago by Friederike3.3k
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Comment: C: Data integration strategies for single cell RNA-seq
... Did you try out the alignment procedure that [Butler et al.](https://www.ncbi.nlm.nih.gov/pubmed/29608179) described? I believe, this [vignette](https://satijalab.org/seurat/immune_alignment.html) might be appropriately similar to your experimental set up to follow along. In short, I would suggest ...
written 11 days ago by Friederike3.3k

Latest awards to Friederike

Scholar 7 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 8 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 8 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 12 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 15 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 22 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 22 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 24 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 25 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 28 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 29 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
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
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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
Scholar 9 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 10 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?
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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

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