The Chicago and PCHiCdata R packages are now part of the new Bioconductor release (3.3).
Their stable versions are now available here:
The chicagoTools scripts are not part of Bioconductor and will continue to be available from our Bitbucket repository:
As Bioconductor releases only happen twice a year, the Bitbucket repository will also continue to host the most recent versions of the R packages.
We welcome Lina Dobnikar from the Cambridge BBSRC DTP PhD programme for her rotation project in the lab. Lina will be using single-cell RNA-seq data analyses to characterise the vascular smooth muscle cell niche.
The promised “next few weeks” since CHiCAGO release have passed, and the paper preprint describing this software is finally out on bioRxiv.
Michiel Thiecke is joining the group as an MRC-funded PhD student. Michiel has a Masters degree in bioinformatics and an impressive number of research internships all over the world under his belt. Welcome!
Our group retreat this year featured science discussions… and bubble football!
Both were a great success, despite the few bruises (from football!) and the pouring rain (which is why it was impossible to take pictures at the pitch). The match has ended in a draw – as a true testament of our team spirit!
We are finally ready to release CHiCAGO, our pipeline for Capture HiC analysis. Led by Jonathan, Paula and Mikhail, and a result of two years of work, this package features a new statistical model and a bespoke multiple testing procedure for calling significant interactions in these challenging data. A preprint describing the algorithm in detail will be available in the next few weeks, but the software and documentation are ready to use!
Phoebe is joining us for her final project as part of the MPhil Computational Biology course. She will be combining single-cell and population-level RNAseq data to study vascular smooth muscle cell biology and then will fly back to the her native USA for a PhD.
Erin joins us as part of her BBSRC DTP studentship. Erin hails from a computer science background with an MEng from UCL and will study lineage plasticity using single-cell RNA-seq data during her rotation. Welcome!
We’re off to a group retreat tomorrow, starting with science discussions in the morning at Jesus College (hosted by Jo). After lunch in town, we then head to Thetford Forest for GoApe.
Update: We’ve survived!
Having successfully completed her rotation project with us, Jo has chosen our lab for her PhD. Needless to say, we are very happy with Jo’s choice!