User: mmfansler

gravatar for mmfansler
mmfansler160
Reputation:
160
Status:
Trusted
Location:
MSKCC | New York, NY
Twitter:
@MervinFansler
Last seen:
2 days, 19 hours ago
Joined:
2 years, 5 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 • 18 results • page 1 of 2 • next >
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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 10 weeks ago by mmfansler160
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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 3 months ago by mmfansler160
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Comment: C: assembly of mouse transcriptome from BAM file
... Just to test, I downloaded a transcriptome from there, unzipped, then indexed (`igvtools index transcriptome.fa`). This loaded fine in IGV. As mentioned by @genomax, we'll need more details to help further. ...
written 3 months ago by mmfansler160
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Comment: C: How to reduce a Python 2.7 dataframe from float 64 to float 8 and then plot the
... First, I'm not aware of a `float8` datatype in **numpy**. Second, in a minimal example, I wasn't able to recreate the issue with `float16`: [](https://photos.app.goo.gl/omoldwIu32pcasD03) Maybe it might be worth adding some example input data for others to test with. ...
written 3 months ago by mmfansler160
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Answer: A: How to setup R into seqmonk when R is intalled via Anaconda?
... From [the **SeqMonk** INSTALL instructions](https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/INSTALL.txt): > If R is installed into your path, such that you can just type 'R' in a > command shell and see an R session started then you don't need to > tell SeqMonk where it is. If ...
written 3 months ago by mmfansler160
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Answer: A: assembly of mouse transcriptome from BAM file
... [mmseq](https://github.com/eturro/mmseq) is a project that has [transcriptomes assembled for the Sanger mouse strains](http://www.bgx.org.uk/data/REL-1303-SNPs_Indels-GRCm38/) as well as tools to do your own assembly if needed (e.g.,[mouse_strain_transcriptome.sh](https://github.com/eturro/mmseq/blo ...
written 3 months ago by mmfansler160
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Answer: A: Bayesian Approach For Polymorphism And Phenotype
... Nothing about this problem seems particularly suggestive of a Bayesian method. Unless, perhaps, one has in mind a prior model (say, preference for shorter motifs over longer ones?). Instead, what do come to mind are **decision trees** and **linear discriminant analysis (LDA)**. In a decision tree ...
written 3 months ago by mmfansler160
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Answer: A: is it meaningless for comparing averages from data with different sample size?
... You can definitely use this kind of data to test the hypothesis that a positive correlation exists, but you need to perform a statistical analysis that uses all the data points and not the means directly. Here are some options I can think of: ### Linear model On the face of it, one might think th ...
written 3 months ago by mmfansler160
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Comment: C: Kallisto read count processed does not tally
... I'm wondering if maybe some of your reads have line breaks in them. Technically, [the FASTQ spec includes this possibility](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/#__sec7title) (like FASTA), and this could cause simple line counting to also be an inaccurate measure. However, it's con ...
written 3 months ago by mmfansler160
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Comment: C: R ggplot Align Y-Axis on multiple graphs
... More of a StackOverflow question: https://stackoverflow.com/questions/24588034/limit-x-and-y-axis-ranges-in-ggplot ...
written 3 months ago by mmfansler160

Latest awards to mmfansler

Scholar 11 days ago, created an answer that has been accepted. For A: is it meaningless for comparing averages from data with different sample size?
Scholar 3 months ago, created an answer that has been accepted. For A: is it meaningless for comparing averages from data with different sample size?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Problem with the installation of Zinba(peak caller) on R
Supporter 3 months ago, voted at least 25 times.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Problem with the installation of Zinba(peak caller) on R
Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.

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