Upgrading R + Bioconductor

Consider this post as a personal note to my future self I have just learnt that Bioconductor developers should NOT always use the development version. On the official website it says: This means that, from mid-October through mid-April, Bioconductor developers should be developing against R-devel. From mid-April to mid-October, developers should use R-release (actually, the R snapshot from the R-x-y-branch) for Bioconductor development. So I needed to change my R version from development to release and I did.

scfind

scfind is a tool that allows one to search large single cell RNA-Seq collections using either cells, gene lists or GO term lists…

Get GSEA done!

Thousands of times I’ve heard of the Gene Set Enrichment Analysis or GSEA. Thousands of times I tried to run it and thousands of times I failed…

How to start working with R

I’ve just come across a great blog post about the best way of starting data analysis in R…

SC3 poster

Some photos from the Functional Genomics & Systems Biology conference…

SC3 - consensus clustering of single cell RNA Seq data

Today I presented the SC3 tool that I am developing for clustering of single-cell RNA-Seq data…

My new paper is out!

My paper ‘Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop’ has been published in Nucleic Acids Research journal…

ISMARA client

ISMARA is a very nice tools that allows one to obtain transcription factor activities from only RNA-Seq or Chip-Seq data…

Bioinformatics Algorithms

Today I received one of the best recent Bioinformatics books - Bioinformatics Algorithms by Phillip Compeau & Pavel Pevzner…

ISMB 2015 Poster

At ISMB-201 in Dublin I presented a poster on my previous PostDoc project: ‘Perturbations of PIP3 signalling trigger a global remodelling of gene expression and reveal a transcriptional feedback loop’…