Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by ssi-dk
A curated list of projects in awesome lists by ssi-dk .
https://github.com/ssi-dk/scdb
R package for maintaining data bases with slowly-changing-dimensions
Last synced: 12 Nov 2024
https://github.com/ssi-dk/genepi-biotrain_virtual_training_7
All data used in the GenEpi-BioTrain Virtual Training 7 session on march 19-20, 2024
Last synced: 12 Nov 2024
https://github.com/ssi-dk/cd-mrg-metabolomics_summerschool_2023
This repository contains teaching material for the 3rd International Summer School on Non-Targeted Metabolomics Data Mining for Biomedical Research
Last synced: 12 Nov 2024
https://github.com/ssi-dk/minilims
LIMS in development to be used in NGS facility
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost-archive
Bacterial Surveillance platform, focused on QC in Denmark
bioinformatics bioinformatics-databases bioinformatics-tool wgs-analysis
Last synced: 12 Nov 2024
https://github.com/ssi-dk/cd-mrg-plateplanner
Python package to create multi-well plate layouts for specimen sample data. Automatically distributes quality control samples according to scheme in config file.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/diseasystore
R package that provides a feature store tailored towards disease modelling
Last synced: 12 Nov 2024
https://github.com/ssi-dk/microreact_integration
Python code for integrating with Microreact
Last synced: 12 Nov 2024
https://github.com/ssi-dk/aeddo
Automated and Early Detection of Disease Outbreaks
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_ssi_stamper
Bifrost Component: SSI Stamper - Runs SSI's QC check on samples using metrics generated from Assemblatron, Min Read Check and Whats my species
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_seqsero
Component for running seqsero in Bifrost
Last synced: 12 Nov 2024
https://github.com/ssi-dk/cd-mrg-bruker
Scripts and documentation for Bruker software
Last synced: 12 Nov 2024
https://github.com/ssi-dk/microbeseq-denmark
Location for SSI's microbial surveillance pipelines
Last synced: 12 Nov 2024
https://github.com/ssi-dk/aef-ddf-diseasystorefhm
Extends diseasystore with Swedish data from Folkhälsomyndigheten
Last synced: 12 Nov 2024
https://github.com/ssi-dk/cd-mrg-fakedata
Notebook showing how to create fake data for our typical case-control studies.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_ariba_resfinder
Bifrost Component: Ariba Resfinder - Runs Ariba on resfinder DB using paired reads
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bps_fbi_scripts_clostyper
Tool to find mge (phages, plasmids, and transposons) in cdiff. Scripts that allow Clostyper to be run in slurm.
cdiff clostridioides-difficile clostyper mge phages plasmids transposons
Last synced: 12 Nov 2024
https://github.com/ssi-dk/cleanrecomb
Cleans putative recombination events from a SNP matrix
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_whats_my_species
Bifrost Component: Whats My Species - Checks species of sample and whether it's correct or not against a kraken DB
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_cge_mlst
Bifrost Component: CGE MLST - Runs kma on a mlst DB using paired reads
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_min_read_check
Bifrost Component: Min Read Check - Checks that provided read files have a minimum number of reads for analysis
Last synced: 12 Nov 2024
https://github.com/ssi-dk/sofi_api
REST API for calling various bioinformatic functionality in SOFI
Last synced: 12 Nov 2024
https://github.com/ssi-dk/beone-datahub
Core web application for the BeONE project.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/infimm-binf-website
BINF website for INFIMM at SSI-DK
bioinformatics computerome scrna-seq
Last synced: 12 Nov 2024
https://github.com/ssi-dk/n_meningitidis_cc11_sgc_sgw
Neisseria Meningitidis CC11 SgC and SgW Nextstrain project
Last synced: 12 Nov 2024
https://github.com/ssi-dk/epidome
Databases, scripts and example data pertaining to the epidome. Subspecies classification of S. epidermidis based on amplicon sequencing.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/read_filtering
Scripts for cleaning of raw read files, human read filtering etc.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/s_aureus_cc9_host_association
Preliminary data, for internal use only!
Last synced: 12 Nov 2024
https://github.com/ssi-dk/prokka_roary_toolbox
Scripts for running prokka and roary on calc.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/punktreskma
SSI wrapper for calling and parsing the output of KMA (Kmer Aligner) for finding point mutations
Last synced: 12 Nov 2024
https://github.com/ssi-dk/flustrain
Consensus sequence generation and subtyping of influenza virus
Last synced: 12 Nov 2024
https://github.com/ssi-dk/project-covid19_subgenomic
Scripts for identification of SARS-CoV-2 subgenomic RNA reads from BAM alignment files and subsequent statistical analyses.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/epidome_2022
Epidome databases and scripts for 2022 update
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_ariba_virulencefinder
Bifrost Component: Ariba Virulencefinder - Runs Ariba on virulencefinder DB against paired reads.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/chewie_datadumper
Simple prototype script for integration of chewieSnake in Bifrost.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_ariba_mlst
Bifrost Component: Ariba MLST - Runs MLST against paired reads using ARIBA
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_ariba_plasmidfinder
Bifrost Component: Ariba PlasmidFinder - Runs Ariba against PlasmidFinder DB using paired reads.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/cc398_global_phylogeny
Preliminary work of CC398 global phylogeny
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_assemblatron
Bifrost Component: Assemblatron - De-novo assembly of paired reads for QC and downstream Analysis purposes
Last synced: 12 Nov 2024
https://github.com/ssi-dk/dash-scroll-up
Dash component to add custom button to scroll to the top of the page.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_sp_ecoli
Ecoli related analysis for the SOFI platform.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/index2rc
Creates illumina samplesheet with the reverse complement of the second index (index2).
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrostapi
Contains the python library for connecting with the bifrost database. Used by bifrost and beone dashboards.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/sofi_core_gitops
GitOps configuration for the sofi_core Kubernetes cluster
Last synced: 12 Nov 2024
https://github.com/ssi-dk/staphylococcal_nasal_occupancy
R scripts accompanying the manuscript "Staphylococcal occupancy within the human nasal microbiota" (Ingham et al.)
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_sp_cdiff
Cdiff related analysis for the SOFI platform.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bifrost_cge_resfinder
Bifrost Component: CGE Resfinder - Runs kma on resfinder DB using paired reads
Last synced: 12 Nov 2024
https://github.com/ssi-dk/microbeseq_nbdev_augment
Files to assist in setup of nbdev
Last synced: 12 Nov 2024
https://github.com/ssi-dk/beone-dashboard
Dashboard developed in React for reading data in BeONE JSON format.
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bps_fbi_fsc_virulencefinder
Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.
assemblies bash ecoli rawreads serotypefinder virulencefinder
Last synced: 12 Nov 2024
https://github.com/ssi-dk/aedseo
Automated and Early Detection of Seasonal Epidemic Onset
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bio_api
REST API for triggering bioinformatic calculations from SOFI
Last synced: 12 Nov 2024
https://github.com/ssi-dk/cdiff_fbi
Typing of Clostridioides difficile isolates using NGS data (reads and contigs) based on tandem repeat loci (TR6, TR10), and toxin genes (cdtA, cdtB, tcdA, tcdB, tcdC).
cdiff fbi tandem-repeats toxins typing
Last synced: 12 Nov 2024
https://github.com/ssi-dk/bps_fbi_sp_ecoli
Ecoli species specific scripts in nbdev2 format.
Last synced: 23 Oct 2024