3DComplex

Hierarchical classification of Protein Complexes

3D Complex is a hierarchical classification of protein complexes that describes similarities in structure, sequence, as well as topology of contacts of the constituent proteins. This is the first automatic method for generating non-redundant sets of complexes, which can be used to derive unbiased statistics on their structure and evolution.

Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA, 3D complex: a structural classification of protein complexes. PLoS Comput Biol. 2006 Nov 17;2(11):e155. Epub 2006 Oct 5


Th-Express

T-Helper Cell Expression Atlas

ThExpress is an integrated expression atlas of single cell RNA-seq T-helper cell types in the mouse immune system.

Stubbington MJT et al.. An Atlas of Mouse CD4+ T cell Transcriptomes. Biology Direct (2015) 10:14

 



TraCeR

Reconstruction of TCR sequences from single-cell RNA-seq data

TraCeR processes single-cell RNA-seq data from T lymphocytes and reconstructs full-length, paired T cell receptor sequences. It can then generate network graphs indicating sharing of sequences between cells.

Michael JT Stubbington, Tapio Lönnberg, Valentina Proserpio, Simon Clare, Anneliese O Speak, Gordon Dougan, Sarah A Teichmann. (2016) T cell fate and clonality inference from single-cell transcriptomes. Nature Methods, 13 329-332


Celloline and Cellity

Single Cell RNA Quality Control and Pipeline

Celloline is a pipeline that handles parallel mapping and quantification of single cell RNA-seq, using standard mapping tools and quantifiers.

The cellity package contains functions to help to identify low quality cells in scRNA-seq data. It extracts biological and technical features from gene expression data that help to detect low quality cells.

Ilicic, T., Kim, J.K., Kolodziejczyk, A.A., Bagger, F.O., McCarthy, D.J., Marioni, J.C., Teichmann, S.A. (2016) Classification of low quality cells from single-cell RNA-seq data. Genome Biology, 17 (1)