Weekly news #9
Table of Contents
News #
Science/Bioinformatics #
Accurate feature selection improves single-cell RNA-seq cell clustering #
Su et al.,Briefings in Bioinformatics 2021
#scrna-seq #feature-selection #clustering
Cell clustering is one of the most important and commonly performed tasks in single-cell RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select a subset of genes (referred to as ‘features’), whose expression patterns will then be used for downstream clustering. A good set of features should include the ones that distinguish different cell types, and the quality of such set could have a significant impact on the clustering accuracy. All existing scRNA-seq clustering tools include a feature selection step relying on some simple unsupervised feature selection methods, mostly based on the statistical moments of gene-wise expression distributions. In this work, we carefully evaluate the impact of feature selection on cell clustering accuracy. In addition, we develop a feature selection algorithm named FEAture SelecTion (FEAST), which provides more representative features. We apply the method on 12 public scRNA-seq datasets and demonstrate that using features selected by FEAST with existing clustering tools significantly improve the clustering accuracy.
Reproducibility in systems biology modelling #
Tiwari et al., Mol Sys Biol 2021
Reproducibility of scientific results is a key element of science and credibility. The lack of reproducibility across many scientific fields has emerged as an important concern. In this piece, we assess mathematical model reproducibility and propose a score card for improving reproducibility in this field.
10 Breakthrough Technologies 2021 #
Technology Review, 24/02/2021
Speeding up machine hearing #
Carney at al., Nat Mach Intell 2021
Computational models that capture the nonlinear processing of the inner ear have been prohibitively slow to use for most machine-hearing systems. A convolutional neural network model replicates hallmark features of cochlear signal processing, potentially enabling real-time applications.
Tools #
jam-systems/jam #
🍞 Jam is an open source alternative to Clubhouse, Twitter Spaces and similar audio spaces.
rxi/lite #
A lightweight text editor written in Lua
xiangpin/ggstar #
⭐ star layer for ggplot2
arrow-py/arrow #
Better dates & times for Python.
Alert yourself after a long-running task in terminal #
Handy little script to notify you after a long job has been finished in terminal.
Guides and Tutorials #
A Vim Guide for Advanced Users #
Are you ready to level up your Vim skills?
Git is my buddy: Effective Git as a solo developer #
If only we all follow these rules.
How to test GitHub actions locally using act? #
You don’t have to force push - just try act.
Gnod/branch-pages #
Example of how to publish each branch in a subdirectory of a GitLab page. Works for public and private projects.
Others #
Massive Google-funded COVID database will track variants and immunity #
Another COVID database resource.
The Technology Behind Cinematic Photos #
How cinematic photos work from Google.
Rust, Zig, and the Futility of “Replacing” C #
Interesting take on mentioned languages to replace C.
Nextcloud faster than ever! Introducing Files High Performance Back-end #
Impressive speed bumps in Nextcloud 21.
Did you know? #
Explanation and implementation of Discrete Fourier Transformation in Julia.