I read the @biorxivpreprint every day. I've recently been asked by various people what/why/how I read so here is a short thread that may be helpful to others: 1/
@biorxivpreprint I read abstracts of articles on the @biorxivpreprint every morning and every evening, and typically a few times during the day as well. I am sometimes delving into the main paper, usually starting with the supplement. 2/
@biorxivpreprint I search for articles on @Google using keywords (and filtering for "past 24 hours"), my lab has @SlackHQ channels where people post articles, I check @rxivist, and I read and search twitter by keywords for topics I'm interested in every day. I follow @biorxivpreprint. 3/
@biorxivpreprint @Google @SlackHQ @rxivist None of these methods is perfect and I have to filter a lot. E.g.. @rxivist can be very useful but I hate their "leaderboards". liorpachter.wordpress.com/2019/01/29/tec… 4/
@biorxivpreprint @Google @SlackHQ @rxivist I find that @Twitter can be very biased, promoting preprints on the basis of popularity of the authors. I try to consciously filter for such bias, specifically seeking out preprint tweets from individuals with few(er) followers who I don't personally know. 5/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I start the process of reading a preprint with the supplement. I begin with a few basic quick checks to establish a prior about the quality the work that I'm looking at. 7/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I check for a data availability statement, and click on the link(s) to see that the data actually exists where claimed. Many preprints don't even have links to data. If I see that going on my prior shifts towards "junk". 8/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I have a big problem with people who are not sharing data. It's not a pet-peeve. It's a serious problem for science and anecdotally a common form of abuse of the @biorxivpreprint. liorpachter.wordpress.com/2019/10/21/zer… 9/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I check for the software. I try to find code that reproduces all the results and figures in the preprint. I do a quick check of the license, the programming language, and I will occasionally download and see if I can get it up and running quickly (I try for a few min. max). 10/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I perform a quick #methodsmatter scan. Most of the time I'm reading in fields I'm familiar with, and I notice whether people are using best-in-class methods. E.g. I'm not impressed if flux capacitor is used in an RNA-seq preprint liorpachter.wordpress.com/2013/10/21/gte… 11/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I can't believe I actually saw that recently. biorxiv.org/content/10.110…
I'm not the police. I'm not trying to get people punished for not using this software or that. If someone is ignoring #methods research it's less likely their science is 🌈 and more likely it's 💩. 12/
I'm not the police. I'm not trying to get people punished for not using this software or that. If someone is ignoring #methods research it's less likely their science is 🌈 and more likely it's 💩. 12/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter Speaking of being familiar with fields, I search every day in all the sites I mentioned for terms including #rnaseq, #scRNAseq, #genomics, #statgen, #popgen, #phylogenetics, #neuroscience, #combinatorics, and recently... #jellyfish. Sometimes other things. 13/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I probably read the @biorxivpreprint a few hours a day. A lot of it happens on my phone between meetings, downtime in various places, etc. I do have to admit sometimes I procrastinate this way. 14/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I make a point to always examine supplementary tables; it's usually just a few seconds to get an idea of what kind of preprint we're talking about by looking there. liorpachter.wordpress.com/2013/09/27/the… 15/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter Weird non-sensical p-values are a common problem in tables. But one can find a lot of dirty laundry in there on quick inspection. BTW same goes for figures. biostat.wisc.edu/~kbroman/topte… 16/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter Speaking of p-values, I always scan quickly to see how many p-value are mentioned (to first order). When I see p=1 or p=0 anywhere🚩. liorpachter.wordpress.com/2015/06/09/pon… 17/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I find a common problem nowadays is people performing multiple-testing correction for their p-values with one multiple testing correction per test. Then the authors report dozens of p-values from different experiments and argue that one of them is significant. 🤔18/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter As far as tables go, pdf tables are 👎. Tables in Excel are also not great. genomebiology.biomedcentral.com/articles/10.11… 19/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I look for a lot of minor detail in the figures just to assess quality before I read seriously: are there labeled axes, coherent plots, captions I can parse without gymnastics etc.? Sometimes, yes. Sometimes no. liorpachter.wordpress.com/2014/04/30/est… 20/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter Now here is one useful trick I learned from a collaborator: I do a quick search for "the the". It's a common typo that is caught if a preprint is properly proofread. There is a surprising correlation between failing "the the" test and preprints even the authors haven't read. 21/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter With a prior at hand l may delve into the preprint. The point of the prior is that it guides me when I'm stuck. If my prior is high I doubt myself and try again. If my prior is low, I wonder whether the problem is with the preprint, not me. This reduces imposter syndrome. 22/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter There is so much material on the @biorxivpreprint now that I can't keep track of most of it anymore. A few years ago I was doing better. The #singlecellRNAseq alone is overwhelming, although focusing on methods papers helps. Still, I know I'm missing lots of good stuff. 23/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter Finally, if I like a preprint I print it out on paper. I've found that reading off paper is really helpful and improves my memory retention. Protip: when *writing* a paper read it *out loud* off a hardcopy to improve the writing. 24/
@biorxivpreprint @Google @SlackHQ @rxivist @Twitter I don't usually take notes but occasionally I save a remark, a tweet about a preprint that I thought was insightful, or a comment someone made in person, with @simplenoteapp. By now I have a large repository of such notes that is easily searchable.
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