Moderator: Friederike

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Friederike5.3k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

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

Posts by Friederike

<prev • 631 results • page 1 of 64 • next >
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Answer: A: Box-Plot for selected gene among different samples using ggplot2
... I concur with everything Wouter has pointed out. That being said, the [`DESeq2` manual](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#plot-counts) may be a good starting point to get you on the right track. And, of course, the [R cookbook](http://www.cookbook-r ...
written 1 day ago by Friederike5.3k
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Answer: A: How to understand the multi-sample processing of Seurat?
... I recommend to read the section about data integration and the usage of the thus normalized data by the Bioconductor folks: In brief, data integration is mostly important for dimensionality reduction and cluster identification where you want to be able to identify **cells** that are very similar t ...
written 1 day ago by Friederike5.3k
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Comment: C: How to understand the multi-sample processing of Seurat?
... The `fastMNN` method is described in detail in the [Bioconductor scRNA-seq book](https://osca.bioconductor.org/integrating-datasets.html) ...
written 1 day ago by Friederike5.3k
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Answer: A: scRNA-seq, Seurat: correlation analysis of two replicates
... I believe you're describing a couple of different features that you'd like to compare in addition to plain ol' correlation. The numbers of detected reads etc. can be assessed via in-built Seurat functions, such as shown in the [basic processing vignette](https://satijalab.org/seurat/v3.1/pbmc3k_tut ...
written 1 day ago by Friederike5.3k
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Answer: A: Boxplots from ChIP-seq Data
... BAM files contain no quantitative information since every entry corresponds to an individual read, its sequence and its location in the genome. In order to compare the number of reads between different regions, you will need to count the number of reads per region in the BED file. It also won't hurt ...
written 1 day ago by Friederike5.3k
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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 11 weeks ago by Friederike5.3k
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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 4 months ago by Friederike5.3k
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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 5 months ago by Friederike5.3k
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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 5 months ago by Friederike5.3k
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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 6 months ago by Friederike5.3k

Latest awards to Friederike

Student 11 weeks ago, asked a question with at least 3 up-votes. For Understanding ATAC-seq data
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Good Answer 11 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?
Scholar 5 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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?
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 7 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 7 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
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: 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
Good Answer 8 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 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 10 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 10 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 10 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 10 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 10 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 10 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 10 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells

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