naturalis/bio-info-docs

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naturalis/bio-info-docs

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Documentation about bioinformatics at Naturalis

openstack-docs

Documentation resources IT facilities Naturalis

wgs2ncbi

Toolkit for preparing genomes for submission to NCBI

sdmdl

Species Distribution Modelling using Deep Learning

mebioda

Course repository for Methods in Biodiversity Analysis

trait-geo-diverse-dl

Ecological Niche Modelling Using Deep Learning

Jupyter Notebook

Hemiphot

Analysis of hemispherical images

imgpheno

Image feature extraction in Python

FormicID

CNN-based image classification of AntWeb images

markdown2scorm

Convert markdown documentation to SCORM

brassicaceae-hybseq-pipeline

HTS-barcode-checker

Pipeline for BLAST analysis of high-throughput DNA sequencing data.

galaxy-tool-taxonmatcher

Find for your input taxonomy the taxonomy from an other database

bio-cipres

Phylogenomic analysis on the CIPRES REST portal

galaxy-tool-lca

arangs

Automated and Reproducible Analysis of Next Generation Sequencing

de-novo-assembly

Contains shell scripts with example usage of NGS assembly tools for mid-size (insect) genomes.

brassica-snps

Ontology-mediated refinement of bulk segregant analyses

biovel-nbc

Naturalis implementations of BioVeL services.

mycorrhiza

Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification - trait data and analysis

barcode-constrained-phylogeny

Pipeline for building topologically-constrained phylogenies from DNA barcode data

trait-geo-diverse-ungulates

Comparative analysis of abiotic niches in Ungulates

img-classify-all

Aggregator repository for projects related to image classification

docker-treepl

Dockerfile for treePL

seshat-trait-data-domesticates

Repository for aggregating comparative trait data for Ungulates and Poaceae and preparing for submission to the SESHAT database

3d-cetacean-scapulae

RiseAndFall

Data repository for the Rise and Fall of Species

mixed-reads-assembly-Erycina

Config files and scripts for assembly of mixed short (Illumina) and long (PacBio) reads

lab-rdm-in-github

Research data management in GitHub

big-data-for-bees

Repository to collect data sets, notes, and prototypes of integration

nbclassify

Proof of concept demonstrating identification of species images using artificial neural networks.

barcode_validator

Standardized validation of barcodes

trap-cap

Captures insect counts on sticky traps by image analysis. Docker image.

Custom-databases-DNA-sequences

Bioinformatics project B19017-555

Galaxy-Pipeline

Wrappers, scripts and configuration files for running cluster and identification analysis on a Galaxy installation.

galaxy-tool-synonym-checker

Use a python script to utilize either the Global Names api or the TNRS api to collect accepted taxonomic names.

tomatogenome

Project directory for the analysis of ancient tomato DNA

orchids

Scripts and data to analyze and visualize duplication and divergence of the MADS box genes in Orchids

monophylizer

A web tool to assess monophyly in trees as produced by BOLD systems

mycodiversity

Pipelines for analyzing fungal diversity

DWCAConfig

DWCA Configuratie bestanden om data te downloaden uit ES (NBA)

butterflies

Data and scripts for a research collaboration with the Vlinderstichting

naturalis-galaxy-tutorials

trait-organismal-ungulates

Morphological, behavioral, and life history traits for the comparative analysis of Ungulates

apexomes

Scripts and config files for mapping and analyzing exomes of the great apes