User: jared.andrews07

gravatar for jared.andrews07
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St. Louis, MO
Website:
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 • 130 results • page 1 of 13 • next >
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Tool: Genotify: Fast, lightweight gene lookup and summarization
... #Genotify: Fast, lightweight gene lookup and summarization Paper: [![status](http://joss.theoj.org/papers/698f9aea23175978e15c4befa2b5f1a1/status.svg)](http://joss.theoj.org/papers/698f9aea23175978e15c4befa2b5f1a1) We are excited to introduce **Genotify**, a light-weight, cross-platform desktop app ...
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Comment: C: distanceToTSS different in HOMER and ChIPseeker annotation
... This would be better posed as a separate question so that you can post the necessary details, along with what you've tried. I'm not super familiar with ChIPseeker, but it seems to me an easy way to do this would be to make sure that the `peak` parameter of the `seq2gene` function only contains your ...
written 1 day ago by jared.andrews07870
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Comment: C: most efficient way to read from large vcf files
... The easiest way is to provide the region(s) you want to extract variants from in a BED file and then use `bedtools intersect`: `bedtools intersect -a myvariants.vcf -b myregions.bed -header -wa > output.vcf` should do the trick. I have no idea if it's as fast as tabix, but it should be pretty qu ...
written 2 days ago by jared.andrews07870
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Comment: C: most efficient way to read from large vcf files
... There is kind of a sister project to this that removes the need for that conversion: https://vcftools.github.io/index.html Tabix is also a good option. Actually, bedtools can do this as well. ...
written 2 days ago by jared.andrews07870
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Answer: A: distanceToTSS different in HOMER and ChIPseeker annotation
... HOMER uses RefSeq annotations by default, while ChIPseeker uses UCSC annotations if you use their default command: ``` peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db") ``` See page 5 of the [org.Hs.eg.db manual](https://bio ...
written 2 days ago by jared.andrews07870
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Answer: A: Which are the regulatory regions among the following?
... Just to be clear, a variant can lie in a coding region and still have regulatory impact. And "regulatory region" can mean different things depending on who you ask. Variants in enhancers may affect their activity as well as any transcripts (eRNAs, lncRNAs) that stem from them. Regardless, if you're ...
written 3 days ago by jared.andrews07870
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Comment: C: Biopython Development on Ubuntu
... Well, it sounds like your edits are probably breaking the code then. Biopython is **very** large, and tinkering with one aspect of it may break it elsewhere in ways that you don't immediately realize. Have you ran Biopython's tests before/after editing the code? ...
written 6 days ago by jared.andrews07870
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Answer: A: Biopython Development on Ubuntu
... The comments have answered your git questions quite well, but I'd also like to point out that you don't need a VM to run Ubuntu on Windows anymore with the release of the [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10). It works very well and I've had no iss ...
written 6 days ago by jared.andrews07870
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Comment: C: Transformed cancer cell-lines RNA-seq database
... A lot of raw sequence data is still controlled access, so you have to jump through some hoops to get it. All the experiments in Expression Atlas have their raw sequencing data in EGA (the European Genome-phenome Archive), and you can usually find the dataset by searching for the Expression Atlas exp ...
written 14 days ago by jared.andrews07870
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Answer: A: Transformed cancer cell-lines RNA-seq database
... I don't know of a database specifically for transformed cell lines - you might be better served by identifying such cell lines and looking for expression data for them. Genentech published RNA-seq for over 600 cell lines [here](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2706), so it's likely at le ...
written 17 days ago by jared.andrews07870

Latest awards to jared.andrews07

Scholar 2 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Supporter 10 weeks ago, voted at least 25 times.
Centurion 5 months ago, created 100 posts.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 8 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 9 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Autobiographer 13 months ago, has more than 80 characters in the information field of the user's profile.

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