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anatomy / WebGL Viewer
Apache License 2.0Public repository containing the code for the open source WebGL viewer based on BabylonJS
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Code used to prepare disease data in survival format, calculate LRC score, data QC and preparation, and data analyses
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Repository containing the script required to reproduce the figure 5 and supplementary figures related to snRNA-seq in cerebrum E14.5
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Sam Nooij / R. gnavus MAGs from rCDI patients
BSD 3-Clause "New" or "Revised" LicenseGenerate metagenome-assembled genomes of Ruminococcus gnavus from recurrent Clostridioides difficile infected patient metagenomes
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Neuroscience / 2020 KeeneKR Multicomponent_T2_EPG
Creative Commons Attribution Non Commercial Share Alike 4.0 InternationalUpdated -
Neuroscience / Standardised ASL Pipeline
Creative Commons Attribution Non Commercial Share Alike 4.0 InternationalUpdated -
Sam Nooij / metagenomics-bacterial-profiling
GNU General Public License v3.0 or laterTaxonomic profiling of metagenomics reads using bacterial and Archaeal marker genes
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Neuroscience / 2021 VeegerTTJ Quantitative muscle ASL
Creative Commons Attribution Non Commercial Share Alike 4.0 InternationalUpdated -
Sam Nooij / Create MAGs from filtered reads-Kraken
BSD 3-Clause "New" or "Revised" LicenseUse Kraken2 to quickly classify metagenomic reads and extract reads of taxa of interest to then assemble metagenomic assembled genomes (MAGs)
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Sam Nooij / metagenomics-scaffold-classification
BSD 2-Clause "Simplified" LicenseAn automated workflow for taxonomically classifying assembled scaffolds from metagenomics data.
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Sam Nooij / cookiecutter-data-science
BSD 2-Clause "Simplified" LicenseUpdated -
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Sam Nooij / metagenomics-plasmid-assembly
BSD 2-Clause "Simplified" LicenseAn automated workflow for generating metagenomic assemblies with a focus on reconstructing plasmids.
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Sam Nooij / screen_pks_in_polyposis_fecal_metagenomes
BSD 2-Clause "Simplified" LicenseScreen fecal metagenomes of polyposis patients for the presence of the pks gene island of procarcinogenic E. coli
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Sam Nooij / FECBUD microbiota analyses
BSD 3-Clause "New" or "Revised" LicenseMicrobiota analyses of metagenomic samples of ulcerative colitis patients and fecal microbiota transplantation donors in the FECBUD trial
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