Obviousness: Rarely Obvious
Pacific Biosciences has made new thrusts in theirongoing intellectual property action against Oxford Nanopore, adding two recently issued patents to the fray. Oxford has publicly brushed these off as"another pore excuse for a lawsuit", but certainly the battle is not over. One of these patents, 9,542,527"Compositions and methods for nucleic acid sequencing", appears to concern using hairpin linkages to read both strands, much likethe 9,404,146"Compositions and methods for nucleic acid sequencing" patent that PacBio led with. Since Oxfordhas announced they will abandon their"2D&...
Source: Omics! Omics! - March 21, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
plexWell: Illumina Libraries by the Plateload
The advent of so-called next generation sequencers, particularly those from Illumina, have brought the price of sequence data down dramatically. However, there is a catch: the cost of preparing DNA to go into the sequencer, the process known as library preparation, has glided downwards on a much shallower trajectory. This means that for projects wishing to sequence very large numbers of small genomes or large constructs the cost of libra ry preparation can be similar to or even exceed the cost of data generation. A small company north of Boston calledseqWell Inc™ has a new approach to Illumina library generation w...
Source: Omics! Omics! - March 19, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
An update to the nhmrcData R package
Just pushed an updated version of my nhmrcData R package to Github. A quick summary of the changes:
In response to feedback, added the packages required for vignette building as dependencies (Imports) – commit
Added 8 new datasets with funding outcomes by gender for 2003 – 2013, created from a spreadsheet that I missed first time around – commit and see the README
Vignette is not yet updated with new examples.
So now you can generate even more depressing charts of funding rates for even more years, such as the one featured on the right (click for full-size).
Enjoy and as ever, let me know if there are ...
Source: What You're Doing Is Rather Desperate - March 15, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics data nhmrc package rstats Source Type: blogs
ONT Updates: GridION X5, PromethION, 1D^2, Scrappie, FPGAs and More
Clive Brown gave a webcast today with updates on a number of Oxford Nanopore topics, but clearly the flagship announcement was a new instrument, GridION X5. Due to the raging snowstorm in the Boston area I was home with my teammate and we've been doggedly going through the tweets (now storified) and my notes (plusDavid Eccles' nice set) to retrieve the juiciest bones therein.Blog team member intently watching@Clive_G_Brown webcast - now must confer& write-up impressionspic.twitter.com/jPGpw1w0lg— Keith Robison (@OmicsOmicsBlog)March 14, 2017Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 13, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
The nhmrcData package: NHMRC funding outcomes data made tidy
Do you like R? Information about Australian biomedical research funding outcomes? Tidy data? If the answers to those questions are “yes”, then you may also like nhmrcData, a collection of datasets derived from funding statistics provided by the Australian National Health & Medical Research Council. It’s also my first R package (more correctly, R data package).
Read on for the details.
1. Installation
The package is hosted at Github and is in a subdirectory of a top-level repository, so it can be installed using the devtools package, then loaded in the usual way:
devtools::install_github("neilf...
Source: What You're Doing Is Rather Desperate - March 8, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics Source Type: blogs
MinION Leviathan Reads: An Update
Last week I posted a piece on some amazing new nanopore data, only to be red-faced to discover the next morning that I had misread the axes. So I re-posted the piece with the offending data and subsequent analysis in strike-thru font. After I did that, I was informed that the same dataset actually did have leviathan rea ds, bigger than my misinterpretation.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 7, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HTML vignettes crashing your RStudio? This may be the reason
Short version: if RStudio on Windows 7 crashes when viewing vignettes in HTML format, it may be because those packages specify knitr::rmarkdown as the vignette engine, instead of knitr::knitr.
Longer version with details – read on.
HTML documentation for broom in RStudioAt work I run RStudio (currently version 1.0.136) on Windows 7 (because I have no choice). This works:
open the Packages tab
click on broom
click on User guides, package vignettes and other documentation
click on HTML to see documentation for broom::broom
HTML documentation for dplyr in RStudioIf I do the same for the dplyr package and choose the ...
Source: What You're Doing Is Rather Desperate - March 6, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics debug rstudio software windows Source Type: blogs
Catching Up On Oxford Nanopore News: More, Better, Meth & Huge
Oxford Nanopore and its collaborators have shown at least three interesting advances in the last few months which I haven't yet covered; the most astounding of which was announced this week. I'll take these three in an order which works logically for me, though it isn't strictly chronological plus I'll touch on some parts of their platform which have not made advances which were perhaps expected.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 1, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Earth BioGenome Project: Ill-Conceived Megaproject Du Jour
There's been a bit of buzz recently about an unfunded proposal to ultimately sequence every living species on Earth, warming up by sequencing every eukaryotic species, with a targeted cost of $4.8B. It pains me a bit to write this, but I'm with those who think this is not a wise way to spend money and certainly not likely to work for anywhere near that budget.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 27, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
#AGBT17 Tweet Archive is Up!
I've used my scheme for collecting and organizing tweets to capture most of the feed from this week's AGBT17 conference. I still need to pore over these in detail, so I won't try to distill out much thoughts (other than single-cell sequencing is clearly in exponential growth phase!).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 16, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Twitter Coverage of the Lorne Genome Conference 2017
Things to know about Lorne in the state of Victoria, Australia.
It’s situated on the Great Ocean Road, a major visitor attraction and a great way to see the scenic coastline of the region
It’s home to a number of life science conferences including Lorne Genome 2017
This week’s project then: use R to analyse coverage of the 2017 meeting on Twitter. I last did something similar for the ISMB meeting in 2012. How things have changed. Back then I prepared PDF reports using Sweave, retrieved tweets using the twitteR package and struggled with dates and time when plotting timelines. This time around I wrote RM...
Source: What You're Doing Is Rather Desperate - February 16, 2017 Category: Bioinformatics Authors: nsaunders Tags: genomics meetings R statistics conference lorne rstudio rtweet twitter Source Type: blogs
Bagging Novel Enzymes Via Mass Spec Metabolomics
Obtaining a complete genome sequence for a bacterium or archean is essentially a solved problem, if you can culture the bug. Grow up biomass, purify the DNA and then use PacBio alone or a combination of long reads (PacBio or Oxford Nanopore) and short reads. These should yield a closed genome with a very low error rate. A few bugs spit at you by repeated failing PacBio sequencing or having some monster prophage or o ther repeat that is longer than the read lengths, but these are very rare. With advances in metagenomics techniques, the solving of uncultured genomes is becoming increasingly easy and many of these rem...
Source: Omics! Omics! - February 12, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Predicting E3 or protease targets with paired protein & gene expression data (negative result)
Cancer datasets as a resource to study cell biologyThe amazing resources that have been developed in the context of cancer biology can serve as tools to study "normal" cell biology. The genetic perturbations that happen in cancer can be viewed almost as natural experiments that we can use to ask varied questions. Different cancer consortia have produced, for the same patient samples or the same cancer cell lines, data that ranges from genomic information, such as exome sequencing, to molecular, cellular and disease traits including gene expression, protein abundance, patient survival and drug responses. These datasets are ...
Source: Evolution of Cellular Networks - February 10, 2017 Category: Cytology Tags: original research Source Type: blogs
On the passing of Hans Rosling
It would be remiss not to mention briefly the passing of Hans Rosling. Data needs storytellers and the world needs advocates for evidence-based decision making. We have lost one of the best.
For some insights into the man and his interesting (and at times challenging) life, I highly recommend this news feature. You can enjoy presentations at the Gapminder website: I’d start with the documentary The Joy of Stats.
Perhaps I should not be surprised or annoyed – but I am – at the lack of coverage this story received at news outlets, particularly in Australia. Aside from an obituary at Guardian Australia (not ...
Source: What You're Doing Is Rather Desperate - February 9, 2017 Category: Bioinformatics Authors: nsaunders Tags: statistics communication gapminder obituary presentations Source Type: blogs
Hyetographs, hydrographs and highcharter
Dual y-axes: yes or no? What about if one of them is also reversed, i.e. values increase from the top of the chart to the bottom?
Judging by this StackOverflow question, hydrologists are fond of both of these things. It asks whether ggplot2 can be used to generate a “rainfall hyetograph and streamflow hydrograph”, which looks like this:
My first thought was “why?” but perhaps, as suggested on Twitter, the chart signifies rain falling from above.
My view (and one held more widely) is that dual axes are to be discouraged unless (1) the variables measured in each case are directly comparable with reg...
Source: What You're Doing Is Rather Desperate - February 6, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics ggplot2 highcharter highcharts hydrology package Source Type: blogs
