Moderator: Friederike

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Friederike5.2k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

<prev • 626 results • page 1 of 63 • next >
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Comment: C: Detecting highly variable genes within replicates
... yes, you can (also see the documentation of either `?DESeq2::rlog` or `?DESeq2::vst` ...
written 12 days ago by Friederike5.2k
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Comment: C: Where can I find public Single Cell RNA-seq data?
... The R package `scRNAseq` provides them in ready-to-use `SingleCellExperiment` objects: [https://www.bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.html#available-data-sets][1] [1]: https://www.bioconductor.org/packages/release/data/experiment/vignettes/scR ...
written 7 weeks ago by Friederike5.2k
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Comment: C: Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
... I agree with Genomax: please post this as a separate question, I'll try to assist there. Please also use the proper formatting for code portions (e.g. make use of the button with 101010) so that it's easier to understand what you did. ...
written 12 weeks ago by Friederike5.2k
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Answer: A: computeMatrix bed format files
... A BED file is a simple tab-separated text file where the first three columns contain the chromosome, start and end position of a specific region of interest. There's a snippet shown in the [deepTools documentation](https://deeptools.readthedocs.io/en/latest/content/help_glossary.html#bed), too. As ...
written 3 months ago by Friederike5.2k
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Comment: C: Single Cell RNA Seq. Analysis
... I also want to point out the truly excellent write-up of numerous people involved in the development of the infrastructure for analyzing scRNA-seq using R packages hosted on bioconductor: ["Orchestrating single-cell analysis"](https://osca.bioconductor.org/) ...
written 3 months ago by Friederike5.2k
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Comment: C: Pull number of cells in cluster from seurat object
... I usually assign the content of the metadata to a separate object, which tends to make subsequent manipulations easier. I am a fan of the [data.table](https://www.listendata.com/2016/10/r-data-table.html) package, but I'm sure there are solutions using the [tidyverse/dplyr](https://dplyr.tidyverse. ...
written 4 months ago by Friederike5.2k
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Comment: C: What is the difference between tissues and cell lines in ENCODE>
... If the origin of the cells is of great importance, you'll definitely have to double check with the actual lab that generated the data. ENCODE is the parent organization for numerous individual labs/grants, and some specialized assays, e.g. ATAC-seq, may be performed on different types of, say, liver ...
written 4 months ago by Friederike5.2k
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Answer: C: What is the difference between tissues and cell lines in ENCODE>
... Cell lines are usually derived from cancerous cells. The ENCODE samples from tissues represent tissues taken from deceased donors (in the case of human data) or wildtype Bl6 mice. I.e. the tissues are probably as close to "healthy" or "normal" tissue as you can get. ...
written 4 months ago by Friederike5.2k
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Comment: C: What is the difference between tissues and cell lines in ENCODE>
... That'll depend on the overall goal of your analysis. For example, if you would like to compare the ENCODE results with some results you or a collaborator have obtained from, say, K562 cells, then it would probably make sense to download those. ...
written 4 months ago by Friederike5.2k
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Comment: C: How to add significant cut off in manhattan plot
... How exactly do you envision it to be added? Just as a number printed on the plot? Or via a line/asterisk/....? ...
written 4 months ago by Friederike5.2k

Latest awards to Friederike

Scholar 3 months 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?
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
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Scholar 6 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
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
Good Answer 6 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 6 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
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 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
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
Scholar 8 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 8 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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
Scholar 8 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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
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
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?

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