User: mmfansler

gravatar for mmfansler
mmfansler240
Reputation:
240
Status:
Trusted
Location:
MSKCC | New York, NY
Twitter:
@MervinFansler
Last seen:
9 hours ago
Joined:
2 years, 9 months ago
Email:
m********@gmail.com

Graduate student in the Mayr Lab at MSKCC as part of the Tri-Institutional PhD Program in Computational Biology and Medicine.  Interested in mRNA biology, particularly in developing computational tools for better characterizing 3' UTR isoform utilization and its role in protein regulation.  Worked in web and software development prior to transitioning to research science.  Trained in CS and mathematics, with specializations in statistics, machine learning, and algebraic topology.

Posts by mmfansler

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Tools for annotating UTRs
... Possible related question: https://www.biostars.org/p/217401/ ...
written 8 weeks ago by mmfansler240
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Answer: A: How can i get a merge fastq file from sratoolkit like the file i directly downlo
... 1. Yes. 2. Don't do that. Instead, use the `--split-spot` flag to extract an interleaved FASTQ. E.g., `fastq-dump --split-spot SRR390728.sra` 3. `fastq-dump` will automatically download from the Sequence Read Archive if you provide the accession instead of a local file. So, in the end you want: ...
written 10 weeks ago by mmfansler240
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Answer: A: Expression of a gene across all cancer datasets
... Check out the [curatedTCGAData package](https://bioconductor.org/packages/release/data/experiment/html/curatedTCGAData.html). It brings together a range of different assays (including RNA expression) and let's you work with only what you need, so you don't have to download everything. [Levi Waldro ...
written 10 weeks ago by mmfansler240
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Comment: C: Finding genome wide annotation R package
... I've never used CellRouter, but their examples show method signatures requiring Bioconductor Organism Packages, so: No, I don't think you can simply substitute a list of TFs. Have you had a look at the vignette I referenced in [my answer](https://www.biostars.org/p/330233/#330269)? Using the NCBI ...
written 11 weeks ago by mmfansler240
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Answer: A: Finding genome wide annotation R package
... If you can't find an existing package/service, you can generate annotation database objects using [the `AnnotationForge` package](https://bioconductor.org/packages/release/bioc/html/AnnotationForge.html). There is [a vignette specifically on constructing `org.xx.eg.db` packages](https://bioconducto ...
written 11 weeks ago by mmfansler240
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Comment: C: Finding genome wide annotation R package
... [The service on dictybase.org](http://dictybase.org/biomart/martview) looks broken to me, and connecting via biomaRt package doesn't seem to work either. ...
written 11 weeks ago by mmfansler240
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Comment: C: Problem with the installation of Zinba(peak caller) on R
... Could you include some of the lines before the error? Specifically, it is useful to see the call to the compiler that generated the error and not just the error. This would help to both verify that the `-std=gnu++98` is properly included and provide us insight into what compiler you're using and th ...
written 3 months ago by mmfansler240
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Comment: C: What is GFF3 and how to extract genomic sequences from it?
... Here are updated links to [the program description][1] and [it's corresponding GitHub repository][2]. [1]: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread [2]: https://github.com/gpertea/gffread ...
written 3 months ago by mmfansler240
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Comment: C: Where Can I Get The Asperasoft Command Line Client Ascp
... This might also be a useful link, since it brings you straight to the download page: [http://downloads.asperasoft.com/en/downloads/8?list](http://downloads.asperasoft.com/en/downloads/8?list) It should also be noted that Aspera no longer offers non-zipped versions of the install script. ...
written 6 months ago by mmfansler240
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Comment: C: Kallisto pseudobam to IGV
... It is optional, but if you want an accurate header in the BAM you should use the `--chromosomes` flag. I tried running without it, and this resulted in all chromosomes being assigned `LN:536870911` in the header. A **chrom.sizes** file is usually readily available. E.g., simple searching "mm10 ch ...
written 7 months ago by mmfansler240

Latest awards to mmfansler

Teacher 25 days ago, created an answer with at least 3 up-votes. For A: is it meaningless for comparing averages from data with different sample size?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Problem with the installation of Zinba(peak caller) on R
Scholar 4 months ago, created an answer that has been accepted. For A: is it meaningless for comparing averages from data with different sample size?
Scholar 7 months ago, created an answer that has been accepted. For A: is it meaningless for comparing averages from data with different sample size?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Problem with the installation of Zinba(peak caller) on R
Supporter 8 months ago, voted at least 25 times.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Problem with the installation of Zinba(peak caller) on R
Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.

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