User: jared.andrews07

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Washington University in St. Louis
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https://github.com/j-a...
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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 • 29 results • page 1 of 3 • next >
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Answer: A: Can you use Python to get download flanking sequences of genes from Ensembl's ol
... You should probably take a look at [pyensembl][1]. This will allow you to pull all the genes for your IDs (along with their chromosome/start sites/strand). Then you can [download the Chicken genome][2] as a FASTA file and use [pyfaidx][3] to pull the sequence around the start site of each gene from ...
written 1 day ago by jared.andrews0780
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Answer: A: Differential ChIP-seq analysis
... [ENCODE][1] has thousands of ChIP-seq samples, including cell lines treated with various compounds and untreated lines. Those are very good sets to play with to get the hang of the things. If you want a more concrete set, you can try the [small set from the `DiffBind` package vignette][2]. [1]: ...
written 2 days ago by jared.andrews0780
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Comment: C: Different results from Enrichr
... Very possible it may ignore the gene symbols if they aren't the official gene symbols, whereas presumably the bed file is pulling the closest gene to the region provided. ...
written 3 days ago by jared.andrews0780
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Comment: C: Selecting genes that best separate between two groups
... How are you clustering the genes? Have you tried any sort of pathway or functional enrichment analyses (GSEA, DAVID, etc) of your differentially expressed genes? What is the ttest method, literally just doing t-tests between your two groups? Personally, I've had good success with `limma` and was ab ...
written 3 days ago by jared.andrews0780
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Answer: A: Genes around open regions
... Personally, I'd use [GREAT][1], as you can just feed it your differential regions and it'll do all sorts of enrichment analyses. If you want to feed it three lists of annotated regions as you describe, you can [use `bedtools closest`][2] with the `-d` option and feed it your regions and a gene list ...
written 8 days ago by jared.andrews0780
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Comment: C: Where to find DNase-seq and RNA-seq assays for various cancer lines?
... Kind of a standard data access request - why you need the data, what you'll use it for, etc etc. I think it took us about two weeks to get access going about it in a pretty casual way. See my edit in the answer for an additional resource. ...
written 8 days ago by jared.andrews0780
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Answer: A: Basic methods in ngs analysis
... This [Github][1] has a very extensive list of tools, methodologies, and information pertaining to ChIP-seq experiments and data analysis. [1]: https://github.com/crazyhottommy/ChIP-seq-analysis ...
written 8 days ago by jared.andrews0780
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Answer: A: Identifying peaks of similar enrichment from ChIP-seq?
... I'd probably just use any of the differential peak enrichment tools and select for peaks that don't meet whatever p-value/signal/FDR/magnitude threshold you use. It'd be pretty easy to do this with [MAnorm][1], [diffBind][2], or [csaw][3] (and many others), I'd think. [1]: http://bcb.dfci.harva ...
written 10 days ago by jared.andrews0780
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Comment: C: Tool to identify recurrent mutations directly from VCF
... Ah, tough luck there. Kinda surprised they haven't done that themselves given what it is. ...
written 12 days ago by jared.andrews0780
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Answer: A: Tool to identify recurrent mutations directly from VCF
... I'm not a huge fan of the tool in general, but [FunSeq2][1] kind of does what you want, though it doesn't have quite the level of precision it seems you're looking for. > RECUR (recurrent genes, regulatory elements and mutations within samples) Example: ‘RECUR=Pseudogene(ENST00000467115.1 ...
written 13 days ago by jared.andrews0780

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