User: mmfansler

gravatar for mmfansler
mmfansler260
Reputation:
260
Status:
Trusted
Location:
MSKCC | New York, NY
Twitter:
@MervinFansler
Last seen:
3 hours ago
Joined:
3 years 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 • 28 results • page 1 of 3 • next >
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Comment: C: Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
... Yes, good point! That is effectively what I do in practice. GNU `parallel` respects the `TMPDIR` environment variable, so if you have that specified to a local scratch disk, that's where the intermediates will go. ...
written 17 days ago by mmfansler260
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Answer: A: Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
... # Two-Stage Multithreaded Version for Sorted BAMs While this thread already has some great answers, I wanted to suggest a parallelized version that is robust to open file limits (e.g., > 4096 files). This requires GNU parallel. ### Code find $BAM_DIR -name '*.bam' | parallel -j8 -N409 ...
written 18 days ago by mmfansler260
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Comment: C: Tools for annotating UTRs
... Possible related question: https://www.biostars.org/p/217401/ ...
written 5 months ago by mmfansler260
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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 5 months ago by mmfansler260
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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 5 months ago by mmfansler260
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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 5 months ago by mmfansler260
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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 5 months ago by mmfansler260
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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 5 months ago by mmfansler260
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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 6 months ago by mmfansler260
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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 6 months ago by mmfansler260

Latest awards to mmfansler

Voter 7 weeks ago, voted more than 100 times.
Teacher 3 months 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 6 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 7 months ago, created an answer that has been accepted. For A: is it meaningless for comparing averages from data with different sample size?
Scholar 10 months ago, created an answer that has been accepted. For A: is it meaningless for comparing averages from data with different sample size?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Problem with the installation of Zinba(peak caller) on R
Supporter 10 months ago, voted at least 25 times.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Problem with the installation of Zinba(peak caller) on R
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.

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