Teaching demos for statistics and ML
- Bayesian updating example of a basic normal distribution
- Statistical distributions
- Decision boundaries, ROC and PR curves
- The Poisson distribution and shrinkage
- Markov chains and HMMs
- Bayesian linear models
- Decision trees and XGBoost
- Penalized linear fitting and elastic net
- Clustering using Leiden
Paper: The CD4 T cell epigenetic JUNB+ state is associated with proliferation and exhaustion [link]
- Interactive viewer for the T cell atlas (Cellxgene)
- The Nando software for interpretable ML on GRNs
- Our modified Pando to output data for Nando
- The original Pando can be found here
- Processed data
- The code to process the data
Paper: Telomemore enables single-cell analysis of cell cycle and chromatin condensation [link]
- Interactive viewer for all B cells (Cellxgene)
- Interactive viewer for all GC B cells specifically (Cellxgene)
- The telomemore software
- Precomputed telomere counts and other code for producing plots
New T cell bulk data viewer
See our new T cell data viewer (alpha/beta), including data also from other labs. Does not yet include all the data from the CRISPR/Th2 paper.
Code for all our work is also made available on our GitHub account.
Paper: Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks [link]
Paper: Genome-wide CRISPR screens in T helper cells reveal pervasive cross-talk between activation and differentiation [link]
- Our database of genes affecting Th2 differentiation (CRISPR hits + time course data)
- Browser for Human endogenous ChIP and ATAC
- Browser for Mouse endogenous ChIP and ATAC
- Browser for Mouse retroviral overexpression and ChIP
- Information about our retroviral sgRNA system
- Hits from our Th2 CRISPR screen, in raw MAGeCK format
Some previous thesis reports (under construction):
- William Rosenbaum – Exploration of Small RNA Sequencing Protocols with a Focus on T-helper Cells
- Mattias Wassbjer – Analysis of the relation between RNA and RBPs using machine learning
PhD work of Johan Henriksson:
- Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps
- The homeobox genes of Caenorhabditis elegans and insights into their spatio-temporal expression dynamics during embryogenesis
4D image data of gene expression during C.elegans embryogenesis
All the raw spatio-temporal recording data has now been deposited at Biostudies S-BIAD191. The recordings are in the Endrov OST format. However, OST is just a collection of PNG and JPEG 2d images, so for a quick peek, any image viewer will do.