Taylor Reiter

@ReiterTaylor

PhD candidate in Food Science at UC Davis. Lab for Data Intensive Biology.

Vrijeme pridruživanja: listopad 2012.

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  1. prije 7 sati

    I would love to hear anything you have to say about using Salmon to quantify amino acid alignments in a BAM file, instead of nucleotide alignments!

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  2. prije 7 sati

    For one of the pipelines I'm working on, I recently used Salmon to quantify proteins in a metagenome...and I'm not sure if this was a very bad idea. I would love to hear if this is a very bad idea, or if it's ok. Pipeline here:

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  3. proslijedio/la je Tweet
    30. sij

    Realtime Spell Check and global replacement in IDE 1.3!! 🥳🙌

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  4. 30. sij

    Making titles in ggplot partially italicized is painful, but necessary for things like gene names. The ggtext package makes titles markdown compatible! ggplot() + ggtitle("My *Title*") + theme(plot.title = element_markdown)

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  5. 30. sij

    The vdiffr package is an extension to the testthat package that allows you to add graphical unit tests. This way, you can have a unit test for your visual output, e.g. for a ggplot.

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  6. 30. sij

    Just learned that adding NULL to a ggplot does nothing...which is super useful when writing functions that wrap ggplot. ggplot(...) + NULL is the same as ggplot(...). Thanks !

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  7. 30. sij

    3. Authoritative story tellers: Fake facts are a real danger. Democratized experts must be viral storytellers. Who would you trust better to diagnose your illness, a data scientist who learned some medicine, or a doctor who learned some data science?

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  8. 30. sij

    2. Public processes: To solve problems with repeatability, we need public processes for analysis. One option is RMarkdown. We don't need papers that we read, we need papers that we run. This requires open sources publishing of resources

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  9. 29. sij

    4. Shiny apps: with the same iframe approach, shiny apps can be used to imbed quiz questions or other interactive boards into a website.

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  10. 29. sij

    2. Gifski: stitches together plots output by code chunk to generate a GIF. This can stitch together ggplots or images. 3. learnR: imbeds a learnR console to create an interactive console window in an html document. Sometimes javascript helps with resizing (iframe resizer)

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  11. 29. sij

    Thank you to and for introducing this framework! I'll be using it as an organizing principle in all of my software projects in and out of R!

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  12. 29. sij

    In R/tidy tool framework, most documentation belongs in the vignette, except for the "reference". The reference combines working and theoretical documentation. roxygen2 can be helpful to generate the reference documentation.

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  13. 29. sij

    Documentation is multipurpose. It needs to span practical application, theoretical underpinnings, be useful for those who are studying or learning, and useful to those who are working or implementing.

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  14. 29. sij

    I'm at this week. I took the Building Tidy Tools workshop earlier this week and want to share some of the things I learned. One of my favorite tidbits was a framework to think about the continuum of documentation.

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  15. 22. sij

    I love this graphic that describes why (meta)genome assemblies break. I took a screenshot of it in May....and forgot to write down where it came from. Does anyone know the source of this wonderful graphic?

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  16. 17. sij

    Thanks to for writing conda_r_skeleton_helper and to for all they do!

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  17. 17. sij

    I use conda to version my environments, but sometimes R packages in my workflow aren't available on conda. showed me how to build a conda-forge package from an R CRAN package. I was surprised by how streamlined it was! Tutorial below.

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  18. 16. sij

    This was followed by a really fun discussion on using tidyr::complete() to get complete cases when using dplyr::group_by(). drew up a nice set of examples in this gist:

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  19. proslijedio/la je Tweet
    16. sij

    My favorite? `sourmash compare` is even faster now, we went from 95s in 2.3.1 to 5s in the 3.x series. Next release: working on improving `sourmash compute` (This graph is from , where we track sourmash performance)

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  20. 15. sij

    Need to download A LOT of fastq files from the SRA? sra-tools fastq-dump can help, but finding the right incantation to get the data in the format you want can be difficult. 's lab at SDSU has a great tutorial. Thanks for finding this!

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