Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by Gregor-Mendel-Institute
A curated list of projects in awesome lists by Gregor-Mendel-Institute .
https://github.com/gregor-mendel-institute/aradeepopsis
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
arabidopsis-thaliana deep-learning nextflow plant-phenotyping scikit-image semantic-segmentation tensorflow
Last synced: 06 Nov 2024
https://github.com/Gregor-Mendel-Institute/aradeepopsis
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
arabidopsis-thaliana deep-learning nextflow plant-phenotyping scikit-image semantic-segmentation tensorflow
Last synced: 03 Aug 2024
https://github.com/gregor-mendel-institute/mlmm
An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/bookend
End-guided RNA assembler
Last synced: 12 Oct 2024
https://github.com/gregor-mendel-institute/trg-imageprocessing
Swarts Lab CNN stuff
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/multlocmixmod
An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/snpmatch
A simple python library to identify the most likely strain from the population
1001genomes arabidopsis arageno genotype genotyping genotyping-by-sequencing pipeline snpmatch snps
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/mtmm
A mixed-model approach for genome-wide association studies of correlated traits in structured populations
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/gwa-portal
Web-app to store an display GWAS studies
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/phenobox-system
The “Phenobox”, a flexible, automated, open-source plant phenotyping solution
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/srna-spike-ins
Contains scripts used to design and analyze small RNA spike-in oligonucleotides as described in Lutzmayer, Enugutti and Nodine (2017) Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data, Scientific Reports
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/swedish-genomes
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/gwar
A collection of R functions to conduct downstream GWAS analysis for arabidopsis thaliana.
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/vbc-cicd-examples
examples for container builds at VBC
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/scanplateseg
Python scripts for detection and alignment of dish in scanned seedling data
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/plotnikova.2019
Custom software used to analyze data and generate figures for Plotnikova et al. (2019, Plant Cell)
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/env_init
Linux Environment Initialisation scripts for Scientific Computing on HPC and Workstation Deployments
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/nanopare
RNA 5' analysis tools for use with the nanoPARE protocol
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/gwaportal-gwas-server
Server for accessing HDF5 files and python analysis from GWA-Portal
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/pisupati-gbm-paper-2022
Supplementary data and notebooks required for the paper.
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/test-data
Repository that stores test datasets for CI testing
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/image-jenkins
Jenkins CasC container image
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/384-snp-assay
384 SNP Illumina assay that can be used as a "universal" genotyping panel for segregating populations and fingerprinting
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/vbc-cicd
VBC Jenkins CICD library
cicd continuous-delivery continuous-integration jenkins jenkins-pipeline
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/araport-athaliana-master-accession-app
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/araport-athaliana-master-accession-table
Araport Community API for accessing the A.thaliana master accession list
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/poolhap
Computational tool for inferring haplotype frequencies from pooled samples
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/jamge_states_2023
Code and data for figures in elife paper
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/kwip-nf
A nextflow pipeline to estimate sample (dis)similarity using kWIP
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/galaxy-guide
Guide for Galaxy at the GMI
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/singularity-jupyterlab-sos
Jupyterlab container with SOS kernels
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/nf-methylpy
Nextflow pipeline for running methylpy
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/proalign
Modified from https://github.com/JAJ256/PROseq_alignment.sh
Last synced: 06 Nov 2024
https://github.com/gregor-mendel-institute/gwaportal-hpc-pipeline
HPC pipeline for GWA-Portal
Last synced: 06 Nov 2024