Review on Deep Learning in Biology and Medicine

Deep neural networks are everywhere. They are revolutionizing our day-to-day lives, and this phenomenon no longer needs any introduction or description. Deep learning is especially suitable to find structures in overwhelming amounts of data. Recently, biological data became exactly that – overwhelming, and application of deep learning toolsets to it indeed looks very natural. You… Read More »

asciinema: record commands in terminal

RE: asciinema.org  (Linux/MacOS) It may be nice to share/show commands being typed on a Text Terminal and embed this simple “movie” within blog or HTML page. It seems that the recording gets uploaded to their web site… Since it’s all text-based the file should be rather small and the clarity of replay very good compared… Read More »

Omics Pipe: An Automated Framework for Next Generation Sequencing Analysis

Re:  pythonhosted.org/omics_pipe Next Gen. data analysis requires many steps, that can be learned one by one, for example running an aligner such as bowtie, tophat or STAR, then handle the SAM/BAM file for subsequent analysis. Once the various steps are understood and if there are new analyzes do be performed routinely, it would be “nice”… Read More »

alternativeto.net: finding alternate software

Re:alternativeto.net What software one uses may be the result of colleague recommendations, using “what others use in the lab,” or haphazardly found options online. Or perhaps it is time to “upgrade” a commercial package and the steep price makes you think twice… The crowdsources software recommendation web site alternativeto.net does just that… just enter the name… Read More »

omictools.com: Search engine for biological data analysis

Re: omictools.com Finding software that is relevant to any biological analysis can be inspired by reading a paper or perhaps searching within Google. The web site https://omictools.com/ contains 16,971 software (omic) tools that are organized in categories shown on the home page. Checking a bit further one can find interesting entries such as: High-throughput sequencing data analysis…… Read More »

A comprehensive comparison of tools for differential ChIP-seq analysis

This recent paper deals with the “space of infinite possibilities” of ChIP-Seq data analysis, focusing on challenges of differential binding analysis. They have underlined multiple challenges in this area (Introduction, page 2) and compared 14 software packages, using both real-world and simulated datasets. The observed differences between the results obtained with different methods were not… Read More »

Shoots, roots and mobile sRNA-related epigenetics

Last week PNAS has published something which would apparently contribute to future textbooks: Mobile small RNAs regulate genome-wide DNA methylation. You think that cutting / physical joining of different plants (grafting) will leave their genomes unaffected, right? Think twice! Authors show that mobile RNA travels between the two species and regulate methylation level of thousands… Read More »