Moderator: jared.andrews07

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jared.andrews076.2k
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Soon to be Bioinformatics Research Scientist at St. Jude Children's Research Hospital studying pediatric brain tumors. Ph.D. at Washington University in St. Louis performing comparative multi-omics studies on B and T cell lymphomas to identify their epigenetic underpinnings. 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 R developer, hater of Perl. 

Posts by jared.andrews07

<prev • 709 results • page 1 of 71 • next >
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Comment: C: Sicer peak calling
... So are you still running into issues or were you just a bit confused about the input/output? ...
written 9 days ago by jared.andrews076.2k
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Answer: A: Sicer peak calling
... Have you read [the manual](https://zanglab.github.io/SICER2/#using-sicer2)? It gives very clear commands as for how to run with a control file (or without): `sicer -t treatment.bam -c control.bam -s hg38 -w 200 -rt 1 -f 150 -egf 0.74 -fdr 0.01 -g 600 -e 1000` Those are the default parameters. You ...
written 9 days ago by jared.andrews076.2k
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Comment: C: Re-arrange conditions in Seurat
... Using `levels` is usually the correct way to handle this. Can you elaborate as to what you mean when you say you broke the Seurat object? ...
written 10 days ago by jared.andrews076.2k
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Comment: C: Salmon building index and quantifying mapping questions
... That step would be performed before Salmon. The resulting FASTQ files will work fine with Salmon. You can install it manually or via bioconda - it should work the same regardless. bioconda will add it to your PATH automatically for the virtual environment, so that's probably the easier method. It s ...
written 10 days ago by jared.andrews076.2k
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Comment: C: How to download matrix of the "GSE73554"
... I have changed this to a "Question" as the "Tutorial" flag is for actual tutorials. Additionally, please use the code formatting button (the one with 1s and 0s) when appropriate, as it makes the code much easier to follow. I have done it for you this time. Lastly, you say your code isn't working. H ...
written 10 days ago by jared.andrews076.2k
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Comment: C: Salmon building index and quantifying mapping questions
... Are you getting an error message? ...
written 10 days ago by jared.andrews076.2k
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Answer: A: SAVE biostars.org from FAKE and unnecesary answers
... You seem to hold some pre-conceived notions as to the responsibilities of moderators and users of this site that aren't entirely correct. > Some of the suggestion provided have no connections with the question > asked or sometimes few people ask questions instead of providing any > clues. ...
written 10 days ago by jared.andrews076.2k
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Comment: C: How to process raw data (.cel files) from GEO and get annotation of genes
... You can access the annotation file directly through [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4685) using the platform number. Download the file there and search for your gene of interest to see if it is included. ...
written 12 days ago by jared.andrews076.2k
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Comment: C: How to process raw data (.cel files) from GEO and get annotation of genes
... Can you post the GEO accession here? Whatever microarray platform is used, you can look up the probe annotations to see if there are any to your gene of interest. If it's an old platform, your gene may not be covered (or may have an old name). ...
written 14 days ago by jared.andrews076.2k
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Answer: A: In Gene ontology and KEGG analysis, What is the biological definition of p-value
... I'm going to link to [another of my previous answers](https://www.biostars.org/p/352631/#352666) that explains the logic behind enrichment analyses. The reason that both p-value and false discovery rates (FDR) are used is to account for statistical issues arising from [multiple testing](https://en.w ...
written 14 days ago by jared.andrews076.2k

Latest awards to jared.andrews07

Scholar 9 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For A: Non-computational challenges in bioinformatics
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: Non-computational challenges in bioinformatics
Appreciated 10 days ago, created a post with more than 5 votes. For A: Target genes of a transcription factor
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Scholar 14 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
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Scholar 16 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
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Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
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Scholar 21 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
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Good Answer 27 days ago, created an answer that was upvoted at least 5 times. For A: Significance in gene ontology terms
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Popular Question 10 weeks ago, created a question with more than 1,000 views. For pytfmpval: Efficient, accurate p-value computation for position weight matrices
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Scholar 12 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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Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Significance in gene ontology terms

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