Naturalis Biodiversity Center

Leiden, the Netherlands

Pinned Repositories

barcode-constrained-phylogeny
Pipeline for building topologically-constrained phylogenies from DNA barcode data
Language:Python2 9 783
FormicID
CNN-based image classification of AntWeb images
Language:Python8 13 300
Hemiphot
Analysis of hemispherical images
Language:R11 15 29
imgpheno
Image feature extraction in Python
Language:Python10 12 1010
markdown2scorm
Convert markdown documentation to SCORM
Language:JavaScript8 12 05
mebioda
Course repository for Methods in Biodiversity Analysis
Language:HTML21 10 5082
sdmdl
Species Distribution Modelling using Deep Learning
Language:Python24 5 811
supersmart
Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
Language:JavaScript17 14 1095
trait-geo-diverse-dl
Ecological Niche Modelling Using Deep Learning
Language:Jupyter Notebook17 14 34
wgs2ncbi
Toolkit for preparing genomes for submission to NCBI
Language:Perl29 7 155

Naturalis Biodiversity Center's Repositories

naturalis/sdmdl
Species Distribution Modelling using Deep Learning
Language:Python24 5 811
naturalis/mebioda
Course repository for Methods in Biodiversity Analysis
Language:HTML21 10 5082
naturalis/galaxy-tool-lca
Language:Python3 12 22
naturalis/galaxy-tool-taxonmatcher
Find for your input taxonomy the taxonomy from an other database
Language:Python3 12 1
naturalis/barcode-constrained-phylogeny
Pipeline for building topologically-constrained phylogenies from DNA barcode data
Language:Python2 9 783
naturalis/barcode_validator
Standardized validation of barcodes
Language:Python1 6 44
naturalis/DWCAConfig
DWCA Configuratie bestanden om data te downloaden uit ES (NBA)
Language:Shell1 17 02
naturalis/mycodiversity
Pipelines for analyzing fungal diversity
Language:Python1 13 01
naturalis/seshat-trait-data-domesticates
Repository for aggregating comparative trait data for Ungulates and Poaceae and preparing for submission to the SESHAT database
1 8 0
naturalis/mtdna-reference-database
Reference database of panels of genomes for population-level aDNA identification
Language:Python0 10 70
naturalis/arise-metabarcoding-biodiversity
ARISE metabarcoding
Language:R10 0
naturalis/arise-soil-pilot-analysis
Repository for statistical analysis of spatial structure in the ARISE soil pilot
Language:Python8 0
naturalis/barcode-classify-protax-fungi
Profiling PROTAX-fungi for quick and coarse classification of ITS metabarcoding reads
Language:Python5 0
naturalis/barcode-classify-transformer
Language:Python1 0
naturalis/barcode-phylogenetic-diversity
Repository for experiments with QIIME-based alpha/beta PD metrics
Language:Python5 0
naturalis/bioblend-test
Example implementation of bioblend galaxy client
Language:Python5 0
naturalis/browbrow
Brownian motion in a browser window
9 8
naturalis/comp-genome-mammals-cmah
Repository for the comparative analysis of CMAH inactivation in Mammalian genomes
Language:Shell7 2
naturalis/DNABERT_S
DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
Language:Python1 0
naturalis/edentity-metabarcoding-phylodiv
Shell scripts for prototyping a QIIME2
Language:Python
naturalis/edentity-sequencer-qc
scripts for comparing sequencer outputs
Language:Python
naturalis/evobio2
EvBio2 UL computer practicum
Language:Shell3 0
naturalis/galaxy-pipeline-hybseq
End-to-end implementation of HybSeq analysis in Naturalis's Galaxy portal
Language:Python11 21
naturalis/galaxy-tool-add-metadata-otutable
Language:Python12 0
naturalis/galaxy-tool-BLAST
A new tool and wrapper for the identification with blastn
Language:Python13 21
naturalis/galaxy-tool-cutadapt
Language:Python12 0
naturalis/galaxy-tool-make-otu-table
Language:Python12 0
naturalis/PROTAX
Software for training probabilistic taxonomic classifier PROTAX
Language:Perl1 0
naturalis/snakemake-parallel-test
Language:Perl5 0
naturalis/sysbio-independent-contrasts
Demonstration of independent contrasts calculations for spider length dimorphism
8 0