Summary:

GAPGOM (novel Gene Annotation Prediction and other GO Metrics) is an R package with tools and algorithms for estimating correlation of gene expression enriched terms in gene sets, and semantic distance between sets of gene ontology (GO) terms. This package has been made for predicting the annotation of un-annotated gene(s), in particular with respect to GO, and testing such predictions. The prediction is done by comparing expression patterns between a query gene and a library of annotated genes, and annotate the query gene by enriched terms from the set of genes with similar expression pattern (often described as "guilt by association").

This project was done as part of an internship in collaboration with the NTNU.

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Summary:

Repository for the XEMCLA (energy-dispersive X-ray Electron Microscopy CLustering Analysis) project, aiming to cluster cell structures in EM images with extra atomic-element xray diffraction matrices/images. A more in depth description about the project can be found in our preliminary and regular report.

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MetaToKrona

Summary:

MetaToKrona is a web-application that combines MetaPhlAn 2 and Kronatools. The reason for this is because Krona plots are interactive and give an easier to understand view of a metagenomic sample than the static plots Metaphlan2 produces. The webtool has a queuing system that allows multiple users to submit their jobs. When a job is done running, you should receive an email with a link to the output.

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Evaluating the best combination of aligners for both single-cell and multi-cell data

Summary:

This project is a general RNA-seq pipeline made for comparing single-cell RNA and multi-cell RNA expression data as close as possible with a certain combination of commands and a combination of aligners and mappers.

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NCBI_SRA_TO_EBI_FASTQ

Summary:

This python script will download .fastq/.fq files from the EBI (http://www.ebi.ac.uk/) using any ftp link of the NCBI (https://www.ncbi.nlm.nih.gov/) containing .sra (Sequence Read Archives file) files. This is, to prevent the need of using the poorly documented fastq-dump (https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump) command line tool and understanding all it's parameters. Also to prevent unneccesary conversion and waste CPU cycles.

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Re-estimating the reproduction numbers of Ebola virus disease (EVD) during the 2014-2016 outbreak in West Africa using a complete dataset.

Summary:

This project aimed to get a better guess at the reproduction numbers of Ebola after the 2014-2016 outbreak in Africa. The original study did not provide a complete dataset as the outbreak was ongoing. We repeated the said study and recalculated the reproduction numbers behind the outbreak.

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LeapingPymol

Summary:

This project aims to combine the Leap sensor with Pymol with help of the Leap SDK and python3.

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