User: jared.andrews07

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jared.andrews071.6k
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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 • 232 results • page 1 of 24 • next >
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Answer: A: What is the reason for big difference in DEGs estimation compared to previous es
... Well, it's not necessarily Tophat, but cufflinks and DESeq2 are very different methodologies. I would not be overly worried if you don't capture 100% of their results. How does it look in the opposite direction (how many of your identified DEGs are in their list)? You can't compare apples to apples ...
written 3 days ago by jared.andrews071.6k
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Comment: C: Biomedical Literature Mining- Steps and Resources
... This [book chapter](https://www.researchgate.net/publication/323220245_Text_Mining_for_Bioinformatics_Using_Biomedical_Literature) provides good background on text mining in biomedical literature in general, with specific sections on almost all of your topics and names of resources that might be hel ...
written 5 days ago by jared.andrews071.6k
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Comment: C: Pathway analysis and Gene enrichment Analysis Queries
... I would likely run all three lists, as you can make different statements about each. For the full list, you can say that enriched pathways are perturbed or deregulated. Maybe the genes are split between up/down regulated. It still provides you something to hypothesize about, though actual effects wo ...
written 5 days ago by jared.andrews071.6k
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Comment: C: Biomedical Literature Mining- Steps and Resources
... Totally thought I put it in there, nice catch. ...
written 5 days ago by jared.andrews071.6k
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Comment: C: Problem installing fcgene using cygwin64.
... That is rough, Windows 10 Subsytem for Linux is really good. It is definitely worth the ~$40 to upgrade if you are going to continually doing bioinformatics on a Windows machine. A VM running Ubuntu is probably your best bet, to be honest. There are a lot of tutorials on how to set them up, and th ...
written 6 days ago by jared.andrews071.6k
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Comment: C: Pathway analysis and Gene enrichment Analysis Queries
... I'm also going to recommend my [very recent answer](https://www.biostars.org/p/352631/#352666) to a similar question for why we do enrichment analyses and how they work. Other resources include [clusterProfiler](https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html) (R) and [enri ...
written 6 days ago by jared.andrews071.6k
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Answer: A: Biomedical Literature Mining- Steps and Resources
... This question is definitely too broad, but [this book](https://www.nltk.org/book/ch03.html) is a decent primer on basic NLP in python. Chapters 3-5 cover your specifically requested tasks. [This review](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5804013/) on generating gene-disease associations ma ...
written 6 days ago by jared.andrews071.6k
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Comment: C: Creating a Venn diagram from RNA seq data
... Oh, okay. If your only real goal is to show similarity between the two stages, something as simple as mentioning the number of differentially expressed genes between the two stages should really suffice, honestly. Venn diagrams aren't really a great construct for gene expression data, in my mind. He ...
written 6 days ago by jared.andrews071.6k
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Answer: A: Significance in gene ontology terms
... Pretty much all gene ontology analysis works the same way and answers the same question - for a given GO term, is your list of genes enriched for association with that term at a significantly higher rate than background? Your background could be all genes or a subset of genes depending on what exact ...
written 6 days ago by jared.andrews071.6k
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Comment: C: Creating a Venn diagram from RNA seq data
... A Venn diagram isn't really going to tell you *which* genes are commonly expressed between conditions, just how many. Are you sure a Venn diagram is what you want? Or are you trying to determine common sets of differentially expressed genes between the different treatment comparisons? Regardless, we ...
written 7 days ago by jared.andrews071.6k

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