Wellcome Sanger Institute
Cellular Genetics Software
Computational tools developed by the research groups and scientific teams of the Cellular Genetics Programme
List of Computational Tools from the Cellular Genetics Programme
Single Cell Computational Tools for Antigen Receptor Reconstruction
| Name | Website |
|---|---|
| TraCeR | https://github.com/Teichlab/tracer |
| TraCeR – reconstruction of T cell receptor sequences from single-cell RNAseq data | |
| BraCeR | https://github.com/Teichlab/bracer |
| BraCeR – reconstruction of B cell receptor sequences from single-cell RNAseq data | |
| KirID | https://github.com/Teichlab/KIRid |
| KIRquant – quantification of KIR genes using personalised references | |
Single Cell and Spatial Analysis Computational Tools
| Name | Website |
|---|---|
| CellPhoneDB | https://www.cellphonedb.org |
| Publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately. | |
| SC3 | http://bioconductor.org/packages/SC3 https://www.sanger.ac.uk/tool/single-cell-consensus-clustering-sc3 |
| SC3 is a method for unsupervised clustering of single-cell RNA-seq data. In addition to a graphical user-interface, SC3 provides additional information about potential outliers and marker genes for each cluster. | |
| D3E | https://sanger.ac.uk/tool/discrete-distributional-differential-expression-d3e |
| D3E is a method for identifying differentially expressed genes from single-cell RNA-seq experiments. D3E compares the full distribution between two sample to identify a set of differentially expressed genes. | |
| MPRAnator | https://sanger.ac.uk/tool/mpranator/ |
| A tool for the design of high-throughput massively parallel reporter assays (MPRAs). | |
| scRNAseq course | https://scrnaseq-course.cog.sanger.ac.uk/website/index.html |
| Teaching material the Hemberg Group’s course on computational analysis of single-cell RNA-seq data. | |
| scRNAseq datasets | https://hemberg-lab.github.io/scRNA.seq.datasets |
| A collection of publicly available datasets used by the Hemberg Group at the Sanger Institute. | |
| cardelino | https://github.com/PMBio/cardelino |
| Clone identification from single-cell data. This R package contains a Bayesian method to infer clonal structure for a population of cells using single-cell RNA-seq data (and possibly other data modalities). | |
| scLVM | https://github.com/PMBio/scLVM |
| scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation. | |
| MNN | https://github.com/MarioniLab/MNN2017 |
| Code for the paper Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours by Haghverdi et al. (2018). | |
| bbknn | https://github.com/Teichlab/bbknn |
| BBKNN is a fast and intuitive batch effect removal tool that can be directly used in the scanpy workflow. | |
| kBET | https://github.com/theislab/kBET |
| An R package to test for batch effects in high-dimensional single-cell RNA sequencing data. | |
| SCCAF | https://github.com/SCCAF/sccaf.github.io |
| Machine learning based self-projection framework to assess the clustering quality of single-cell RNA-seq data, find similar cell clusters that encode identical signature, detect potential doublets and find marker genes. | |
| scfind | https://scfind.sanger.ac.uk/ |
| Search engine for genes in large single-cell sequencing collections. | |
| scmap | https://scmap.sanger.ac.uk/ |
| A method for projecting cells from a scRNA-seq experiment onto the cell-types or individual cells identified in other experiments | |
CRISPR/Cas9
| Name | Website |
|---|---|
| FORECasT | https://partslab.sanger.ac.uk/FORECasT |
| FORECasT is a tool for predicting the mutational outcomes resulting from double stranded breaks induced by CRISPR/Cas9. | |
| JACKS | https://partslab.sanger.ac.uk/JACKS |
| JACKS: joint analysis of CRISPR/Cas9 knockout screens. | |
Other tools
| Name | Website |
|---|---|
| spatialDE | https://github.com/Teichlab/SpatialDE |
| SpatialDE is a method to identify genes which significantly depend on spatial coordinates in non-linear and non-parametric ways. | |
Wellcome Sanger Institute