User: jared.andrews07

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jared.andrews071.3k
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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 and fledgling developer. Strange fascination with ostriches.

Posts by jared.andrews07

<prev • 199 results • page 1 of 20 • next >
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Answer: A: cell type specific TAD coordinates and orientations for Hi-C
... The [4D Nucleome project](https://data.4dnucleome.org/) is the best repository for this sort of data I've found. Be sure to tick the little "Show External Data" widget for a full view. What do you mean by TAD orientation? For coordinates, your best bet is to go hunt for the publication for whateve ...
written 2 days ago by jared.andrews071.3k
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Comment: C: The difference between heatmap.2 and pheatmap
... As @h.mon said, you can change the clustering algorithms for each quite easily - you should be able to derive essentially the same heatmap from each with a few tweaks. Both are fine for heatmap generation of expression data. It sounds like you might not be scaling by row or just not clustering the c ...
written 3 days ago by jared.andrews071.3k
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Answer: A: How to convert MEME MOTIF to all potential sequences?
... This can easily by done with biopython, see this [answer on StackOverflow](https://stackoverflow.com/questions/27551921/how-to-extend-ambiguous-dna-sequence) for full code/explanation. I've posted the necessary function below. from Bio import Seq from itertools import product def e ...
written 4 days ago by jared.andrews071.3k
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Comment: C: 2 peak files in plotAvgProf2 [ChIPseeker]
... I think the peak files need to be passed in as a `list`. Also, be sure to recognize that all of ChIPSeeker's average peak profiles just show the number/frequency of peaks, **not the number of reads**. The vignette is slightly confusing in that regarding since all of the y-axis labels are "Read Coun ...
written 8 days ago by jared.andrews071.3k
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Comment: C: Does it make sense to consider a genomic loci when there is no peak but high sig
... Right, the ratios might be based on those counts, but ratios are often misleading. I'd try making the same panels with the log2 normalized counts - I think this will be more convincing than the ratios. Merging sites from B into A selectively could be done, but you need to be careful to set strict ru ...
written 9 days ago by jared.andrews071.3k
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Comment: C: Does it make sense to consider a genomic loci when there is no peak but high sig
... And by lowering, I guess I really meant raising the q-value threshold (maybe try 0.05?). I'm not sure what you mean by "merge them to panel A" in your main question. You mean remove them from the P3 specific list? There could be a lot of reasons you're seeing what you're seeing. A few things to con ...
written 9 days ago by jared.andrews071.3k
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Comment: C: Does it make sense to consider a genomic loci when there is no peak but high sig
... Ah, MAnorm isn't bad either. For single replicate comparisons, it's as good a tool as I've seen. Sounds like peak calling may be your issue. What parameters are you using with MACS? You can try lowering the q-value threshold and decreasing the lower bound on the mfold setting, which should increase ...
written 9 days ago by jared.andrews071.3k
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Answer: A: Does it make sense to consider a genomic loci when there is no peak but high sig
... Peak calling tends to vary so much from sample to sample that for cases like this, I usually end up deriving a consensus peakset for all samples and getting signal in that peakset across all samples before comparing across them. [DiffBind](https://bioconductor.org/packages/release/bioc/html/DiffBind ...
written 9 days ago by jared.andrews071.3k
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Answer: A: How can I find motifs under individual ATAC-peaks?
... The [MEME suite](http://meme-suite.org/index.html) provides both [motif scanning](http://meme-suite.org/tools/fimo) and [motif enrichment](http://meme-suite.org/tools/ame) tools (among many others). It's probably the most comprehensive motif toolset out there, imo. Motif scanning inherently yields ...
written 10 days ago by jared.andrews071.3k
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Comment: C: Visualization of a gene expression data
... What do you mean by "visualize them in Encode"? Can you post a few lines so we can see what format the file is in? What is your purpose and what do you want to show? ...
written 23 days ago by jared.andrews071.3k

Latest awards to jared.andrews07

Scholar 25 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 4 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?
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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 C: Combining vcf files so that same loci data is combined
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