Databases and Software
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.
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.
Embryonic stem cell gene expression database
ESpresso is a database for querying gene expression in mouse embryonic stem cells.
Single-Cell RNA-sequencing of Pluripotent States Unlocks Modular Transcriptional Variation Kolodziejczyk A.A.1,2*, Kim, J.K.2, Tsang, J2, Illicic, T. 1,2, Henriksson, J.1, Natarajan K. N.1,2, Tuck A.C.1,2, Gao X2, Bühler M3, Liu, P.2, Marioni, J.C.1,2+ and Teichmann, S.A.1,2+ Cell Stem Cell 2015
Further, the database compares our data with data from:
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
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)