User: jared.andrews07

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jared.andrews072.5k
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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 • 318 results • page 1 of 32 • next >
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Comment: C: Imputation of scRNA-seq data
... For Seurat, you want the [RunALRA](https://www.rdocumentation.org/packages/Seurat/versions/3.0.2/topics/RunALRA) function. I've never used it, but I think that replaced the old AddImputedScore function. ...
written 3 days ago by jared.andrews072.5k
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Comment: C: Integrating VDJ sequencing data with Seurat
... Also, it may be worthwhile to remove/ignore columns from your VDJ data that are `FALSE` or `None` in the "productive" column, as you'll end up with a lot of extra noise otherwise. Actually, it might be best to just get the clonotype id for each cell, then get the gene information from the `consensus ...
written 5 days ago by jared.andrews072.5k
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Comment: C: Integrating VDJ sequencing data with Seurat
... Hey, this is great! One note would be that you don't need to manually add the sample prefix to the barcode in your first step. You can use `add.cell.ids` when you perform the `merge` step. ...
written 6 days ago by jared.andrews072.5k
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Comment: C: Bioinformatics Workstation Suggestions
... The 1080 is likely wasted money unless you're doing protein structure modeling or something along those lines. 64 GB memory should be sufficient for most scRNA datasets <100k cells. And there are ways to do larger analyses by using the loom format, etc. What you have sounds fine otherwise. RAM ...
written 10 days ago by jared.andrews072.5k
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Answer: A: scRNA Cell Type ID web resources
... [CellMarker](http://biocc.hrbmu.edu.cn/CellMarker/) is decent for trying to determine, well, cell markers. Has lots of tissues and cell types from both single cell and bulk studies. [PanglaoDB](https://panglaodb.se/search.html) is similar, but lets you search with gene sets as well. It only uses s ...
written 11 days ago by jared.andrews072.5k
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Comment: C: GO enrichment analysis from peaks to corresponding genes for each MSigDB Oncogen
... You need to change the `ontology` to whatever ontology that term/pathway would be found in and then change the `termID` to whatever the ID for the pathway is. ...
written 11 days ago by jared.andrews072.5k
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Answer: A: GO enrichment analysis from peaks to corresponding genes for each MSigDB Oncogen
... That is much more clear, thank you. And you're right, apparently there isn't a great approach to getting the genes in each enriched pathway. The only way that I can see to do it is by looking at each pathway you're interested in individually. A bit of a hassle, but you could write a function to do ...
written 11 days ago by jared.andrews072.5k
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Comment: C: GO enrichment analysis from peaks to corresponding genes for each MSigDB Oncogen
... What have you tried? What final output do you want? We need hard examples of what you have, what you've tried, and what you expect to get out at the end. We can't help you much otherwise. ...
written 13 days ago by jared.andrews072.5k
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Comment: C: Associating VDJ clonotyping data with scRNA-seq in Seurat
... Thanks for the addition. Yeah, I actually went back to v2 to figure it out. I'm not quite sure why they changed the documentation to something that's (imo) more confusing, but you're dead-on that it's really simple once you realize it's just a data frame. ...
written 18 days ago by jared.andrews072.5k
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Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
... Single cell technologies are booming, but figuring out how to integrate multimodal data sets is certainly still a challenge, even with well-supported and constantly updated software (like Seurat). I struggled to find any info as to how to associate my Chromium 10X TCR-sequencing data with the corres ...
tcr rna-seq tutorial single cell seurat written 19 days ago by jared.andrews072.5k • updated 10 days ago by atakanekiz130

Latest awards to jared.andrews07

Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Commentator 10 days ago, created a comment with at least 3 up-votes. For C: How to choose good tools for identifying functional SNPs?
Scholar 10 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 11 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Scholar 26 days 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?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 9 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: How to choose good tools for identifying functional SNPs?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 5 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: How to choose good tools for identifying functional SNPs?
Scholar 6 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 7 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 7 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 9 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?

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