Moderator: jared.andrews07

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jared.andrews075.2k
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St. Louis, MO
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Ph.D. candidate at Washington University in St. Louis. I have a strong interest in the development of high-performance, flexible bioinformatic tools that can integrate multiple -omics datasets to yield interesting and plausible conclusions that can then be experimentally validated.

Avid Python user, fledgling developer, hater of Perl. 

Posts by jared.andrews07

<prev • 634 results • page 1 of 64 • next >
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Comment: C: How to annotate edgeR results?
... What do you mean by "functionally annotate"? What information are you trying to add? Can you give an example of your desired output? ...
written 21 hours ago by jared.andrews075.2k
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Answer: A: Looking for suggestions if ROSE can handle multiple samples together?
... If they are biological replicates, I'd recommend running ROSE on each separately and then comparing overlap and signal with bedtools/diffbind/csaw. When comparing SEs, signal changes over such large windows often dilutes the fold changes that you'll get from most approaches. In my opinion, the best ...
written 21 hours ago by jared.andrews075.2k
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Comment: C: scRNA-seq, Seurat: correlation analysis of two replicates
... I second this method - it is by far the easiest way. You can see how to do so in a single line in the [Seurat cheat sheet](https://satijalab.org/seurat/essential_commands.html). After doing so, you can just plot after performing dimensionality reduction by PCA/TSNE/UMAP and color by replicate to ass ...
written 1 day ago by jared.andrews075.2k
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Comment: C: Best statistical test when plotting normalised counts
... DESeq2 should handle any batch effects in the model itself for differential gene expression, so there is no need to use `combat` or `sva` for getting your list of DEGs. Use the `dds` object. I would try the DESeq2 output for visualization first too - there isn't much point trying to deal with batch ...
written 7 days ago by jared.andrews075.2k
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Comment: C: Best statistical test when plotting normalised counts
... I generally dislike limma's `removeBatchEffect` function, as it directly affects your base counts. Accounting for this in your design formula is typically enough for DGE, though I suppose for visualization, it may prove useful to use the limma function at times. I don't see anything particularly wro ...
written 8 days ago by jared.andrews075.2k
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Comment: C: RNA type recognize
... What have you tried? There are lots of ways for looking for this - intron inclusion and polyA tails likely the lowest hanging fruit. ...
written 11 days ago by jared.andrews075.2k
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Answer: A: QC of fastq files from SRA
... Is it safe? Yes. Is it necessary? Run them through FastQC to see if they've been trimmed or have adapters detected. ...
written 12 days ago by jared.andrews075.2k
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Comment: C: Chip-Seq input normalization with deeptools
... What did you ChIP? If it's a TF, that wouldn't be surprising that input is occasionally higher than IP. Do you have good peaks? ...
written 12 days ago by jared.andrews075.2k
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Comment: C: Skipping Clustering in Seurat
... Yes. Make your Seurat object, then perform those steps. ...
written 13 days ago by jared.andrews075.2k
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Answer: A: Chip-Seq input normalization with deeptools
... In general, using a method that actually performs valid statistical comparisons of the sample groups at specified positions (like `csaw` or `diffBind`) is the proper way to go about this. They take input into account, and then your average profiles are just a way to show that statistically significa ...
written 13 days ago by jared.andrews075.2k

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Scholar 7 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
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Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Significance in gene ontology terms
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Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Significance in gene ontology terms
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Significance in gene ontology terms
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Significance in gene ontology terms
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Significance in gene ontology terms
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?

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