darogan

clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

ComplexHeatmap

make complex heatmaps as well as self define annotation graphics

ExploringRNAConformationalSpace

Supplementary Materials: For Exploring RNA Conformational Space Under Sparse Distance Restraints

labrador

A web based tool to manage and automate the processing of publicly available datasets.

2018-Balmas-Colucci

RNA-Seq Analysis Scripts to accompany: Balmas, E., et al (2018) Maternal group 2 innate lymphoid cells control fetal growth and protect from endotoxin-induced abortion in mice. doi:https://doi.org/10.1101/348755

AFS_st547_0002

ASE_Meta_Analysis

ASE_Meta_Analysis

Kyprianou_Zernika-Goetz

Kyprianou, C., Christodoulou, N., Hamilton, R.S., Nahaboo, W., Boomgaard, D., Amadei, G., Migeotte, I. & Zernicka-Goetz, M.i (2020) Basement membrane remodelling regulates mouse embryogenesis. https://doi.org/10.1038/s41586-020-2264-2

ParticleStats

ParticleStats: Open source software for the analysis of intracellular particle motility and cytoskeletal polarity

Tristetraprolin_Pisapia_DelPozzo

Pisapia, L., Hamilton, R.S., D’Agostino, V, Pasqualea, B., Strazzullo, M., Provenzano, A., Gianfrani, C. & Del Pozzo, G. (2018) Tristetraprolin/ZFP36 regulates the turnover of autoimmune-associated HLA-DQ mRNAs. DOI:https://doi.org/10.1101/337907

2018-Filipovic-Colucci

RNA-Seq Analysis Scripts to accompany: Filipovic, (2018) Molecular definition of group 1 innate lymphoid cells in the mouse uterus. [Nature Communications, https://doi.org/10.1038/s41467-018-06918-3][bioRxiv, https://doi.org/10.1101/330068]

2018-Turco-Moffett

Turco, M.Y. et al (2018) Trophoblast organoids as a model for maternal–fetal interactions during human placentation. Nature. https://doi.org/10.1038/s41586-018-0753-3

2018_Bacon_Charnock-Jones

Bacon, W.A., Hamilton, R.S., Yu, Z., Kieckbusch, J., Hawkes, D., Krzak, A., Abell, C., Colucci, F. & Charnock-Jones, D.S. (2018) Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice. Front. Immunol., 9:2523 https://doi.org/10.3389/fimmu.2018.02523

2020_Prater_Cindrova

Preflow vs Postflow RNA-seq

Blake_Watson

Genetic disruption of folate metabolism causes epigenetic instability in sperm and distinguishes HIRA as a biomarker of maternal epigenetic inheritance

ConstructingComputationalPipelines

Ong, C-K & Hamilton, R.S. (2018) Constructing Computational Pipelines Encyclopedia of Bioinformatics and Computational Biology, 3, 135-143 https://doi.org/10.1016/B978-0-12-809633-8.20090-3

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

DropSeq_Demultiplex_Trimming

Custom Protocols for Demultiplexing and Trimming raw DropSeq experiment fastq files

First-Second-Trimester-Methylation

Prater, M., Hamilton, R.S., Yung, H-W, Sharkey, A.M., Robson, P, Jauniaux, E., Charnock-Jones, D.S., Burton G.J. & Cindrova-Davies, T. (2020) RNA-Seq reveals changes in human placental metabolism, transport and endocrinology function in the first-second trimester transition. Submitted

igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer

KI_Strunz_Bjorkstrom

MetEor_Project

MetEor: Metastable Epialleles on Request

pycircstat

Toolbox for circular statistics with Python

Ribosomal-Protein

Analysing the positions of ribosomal proteins in the ribosome 3D structure

RNA2DSearch

RNA2DSearch is an open source bioinformatics pipeline for searching for RNA secondary structures involved in RNA localization on a genomic scale.

Sherman

A simple Bisulfite FastQ Read Simulator (BiQRS)