Welcome to our Swan Song for the summer! Today we’re going to be learning the basics of machine learning in Python with our handy-dandy Jupyter notebooks and the 2016 elections and demographics data. Here’s today’s package. Since we’re only doing linear regression plots today, please install seaborn: conda install seaborn
We’re continuing our data explorations of the 2016 US primary elections data, but we’ll begin with a review of the important stuff from last week. Today is when the cool stuff begins because we’ll be playing with merging data from different sources and plotting the data to see interesting trends. If you haven’t already, please … More Data Wrangling in Python, Part II
Today it’s time to introduce probably the best programming language of all time, Python! Python is a powerful toolset that comes with a thriving community of scientific programmers who are making new tools for you to enjoy every day. But first! We need to get a grasp on the basics and start looking at some … More Data Wrangling in Python, Part I
We will go over ImageJ/Fiji macros where we will explain the macro language syntax and go over an example of an image analysis pipeline that is written in a macro. Download the files here!
We’re speeding into our third module of the summer today with something completely different: image analysis! If you have hundreds of images that have to select ROIs for and dread doing it by hand, today we’ll teach you the basics of automation, including how to chug through everything in a folder and process them uniformly … More Image analysis with ImageJ and Fiji, Part I kicks off
As many of us biologists know, heatmaps are so common in papers about any kind of high-throughput assay that they’re almost a cliché. The reason is that they let you view, at a glance, global patterns of differences between clusters of samples and/or genes, allowing you to see the forest instead of the trees (to … More Intro to R III: heatmaps!
Our intro to R continues – this week Bhish will take you through building a simple qPCR analysis pipeline! … More Intro to R: Part II
R is programming language and software environment typically used for statistics and data mining. Unlike some other software used for similar purposes, like Matlab, R is open source, meaning free! For the next 3 weeks, Bhish will walk you through the ins and outs of programming in R, starting today with an introduction, which can … More Intro to R
IGV is a neat graphical software application that takes the sort of files (BAM, BED, bigWig, etc.) you typically get from your friendly neighborhood sequencer and allows you to browse them on your desktop. With BAM files (binary files of alignments), it’s especially handy because you can see each read and where it was placed. … More Genome exploration with IGV
The first thing every data wrangler needs is a full toolbox. Our favorite tools for beginners are IDEs, which are visual interfaces to programming languages. If you’re coming next week, please download IGV, the Interactive Genome Viewer. They’re probably going to make you login first. If you plan on doing the R module or the … More Welcome! Now install some stuff.