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These files contain the SPIRIT checklist and study flow diagram for the SONIA Trial. This trial is a pragmatic randomized controlled trial of standard care versus steroids plus standard care for treatment of pneumonia in adults admitted to Kenyan hospitals.

Data and analysis code to accompany the publication Uncertainty in denoising of MRSI using low rank methods Clarke WT, Chiew M. Uncertainty in denoising of MRSI using low-rank methods. Magnetic Resonance in Medicine 2022;87:574–588 doi: 10.1002/mrm.29018. This submission is hosted and developed on the Wellcome Centre for Integrative Neuroimaging GitLab.

Background: Injecting drugs substantially increases the risk of hepatitis C virus (HCV) infection and is common in vulnerable population groups, such as the homeless and prisoners. Capturing accurate data on relative genotype distribution within these groups is essential to inform strategies to reduce HCV transmission. The aim of this study was to utilize a next-generation whole-genome sequencing method recently validated by Public Health England, in order to produce near complete HCV genomes. This questionnaire was provided to all individual who consented for their participation to the study.

Code (R) for algorithm of rapid diagnosis of HIV-associated tuberculosis in the emergency centre

TRIPOD checklist for manuscript entitled 'A multi-parameter diagnostic clinical decision tree for the rapid diagnosis of tuberculosis in HIV-positive patients presenting to an emergency centre'.

Extended data files for a publication entitled "Evolutionary analysis of the most polymorphic gene family in falciparum malaria"

A design for a tracking collar to attach NDI tracked objects (NDI Polaris Spectra/Vicra/Vega) onto a Storz stereo laparoscope. Archive contains open scad design files and an stl file for 3D printing. The collar was used to support data collection for Thompson, S., Schneider, C., Bosi, M. et al. Int J CARS (2018) 13: 865. https://doi.org/10.1007/s11548-018-1761-3

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

This zip archive contains project-specific data and metadata. Combined with the ANIMA source code (10.5281/zenodo.1163398) and run in the anima Docker container (10.5281/zenodo.1161476), this will allow complete reproducibility of the ANIMA project.

This zip archive contains the complete output of the ANIMA_build.R script. It is structured as follows: The top level contains a zip archive of the ANIMA database (to be copied to the correct location in the ANIMA file tree) Output files of the entire microarray analysis pipeline underpinning ANIMA are included here (mainly plots saved ad pdf and tabular outputs saved as csv)