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@nomad421 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!Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
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. https://taylorreiter.github.io/2020-02-04-How-do-I-quantify-amino-acid-sequences-from-a-metagenome/ … Pipeline here:https://github.com/taylorreiter/2020-aa-abund …
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Taylor Reiter proslijedio/la je Tweet
Realtime Spell Check and global replacement in
@rstudio IDE 1.3!!
#rstudioconf2020#rstudioconfpic.twitter.com/6cICDvWbdq
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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)
@ClausWilke https://github.com/wilkelab/ggtext#rstudioconf2020Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
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.
@paleolimbot#rstudioconf2020Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
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
@paleolimbot!#rstudioconf2020Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
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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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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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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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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Thank you to
@cvwickham and@hadleywickham for introducing this framework! I'll be using it as an organizing principle in all of my software projects in and out of R!Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
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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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.pic.twitter.com/GGyAwfwQG3
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I'm at
#rstudioconf2020 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.pic.twitter.com/8jUlan0oV1
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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?pic.twitter.com/QSG09EsO2F
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Thanks to
@bjoerngruening for writing conda_r_skeleton_helper and to@condaforge for all they do!https://github.com/bgruening/conda_r_skeleton_helper …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
I use conda to version my environments, but sometimes R packages in my workflow aren't available on conda.
@luizirber showed me how to build a conda-forge package from an R CRAN package. I was surprised by how streamlined it was! Tutorial below.https://taylorreiter.github.io/2020-01-16-Building-a-conda-forge-package-from-an-R-CRAN-package/ …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
This was followed by a really fun discussion on using tidyr::complete() to get complete cases when using dplyr::group_by().
@riverpeek drew up a nice set of examples in this gist: https://gist.github.com/ryanpeek/e3185e4cd6ffd55c9dc097726a275505 …https://twitter.com/riverpeek/status/1217878681961414656 …
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Taylor Reiter proslijedio/la je Tweet
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 https://github.com/luizirber/sourmash_resources/tree/c02e9bbe4e533f0a0fa29bd6d8b66375decb4389 …, where we track sourmash performance)pic.twitter.com/NeZFyVpvBR
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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.
@linsalrob's lab at SDSU has a great tutorial. https://edwards.sdsu.edu/research/fastq-dump/ … Thanks@luizirber for finding this!Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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