Pinned Repositories
2018-PlacentalBiologyCourse
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
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
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
labrador
A web based tool to manage and automate the processing of publicly available datasets.
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
darogan's Repositories
darogan/clusterflow
A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
darogan/ComplexHeatmap
make complex heatmaps as well as self define annotation graphics
darogan/ExploringRNAConformationalSpace
Supplementary Materials: For Exploring RNA Conformational Space Under Sparse Distance Restraints
darogan/labrador
A web based tool to manage and automate the processing of publicly available datasets.
darogan/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
darogan/AFS_st547_0002
darogan/ASE_Meta_Analysis
ASE_Meta_Analysis
darogan/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
darogan/ParticleStats
ParticleStats: Open source software for the analysis of intracellular particle motility and cytoskeletal polarity
darogan/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
darogan/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]
darogan/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
darogan/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
darogan/2020_Prater_Cindrova
Preflow vs Postflow RNA-seq
darogan/Blake_Watson
Genetic disruption of folate metabolism causes epigenetic instability in sperm and distinguishes HIRA as a biomarker of maternal epigenetic inheritance
darogan/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
darogan/d3
Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:
darogan/DropSeq_Demultiplex_Trimming
Custom Protocols for Demultiplexing and Trimming raw DropSeq experiment fastq files
darogan/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
darogan/igv.js
Embeddable genomic visualization component based on the Integrative Genomics Viewer
darogan/KI_Strunz_Bjorkstrom
darogan/MetEor_Project
MetEor: Metastable Epialleles on Request
darogan/pycircstat
Toolbox for circular statistics with Python
darogan/Ribosomal-Protein
Analysing the positions of ribosomal proteins in the ribosome 3D structure
darogan/RNA2DSearch
RNA2DSearch is an open source bioinformatics pipeline for searching for RNA secondary structures involved in RNA localization on a genomic scale.
darogan/Sherman
A simple Bisulfite FastQ Read Simulator (BiQRS)