fungi

There are 4 repositories under fungi topic.

MushroomObserver / mushroom-observer
A website for sharing observations of mushrooms.
fungi mushrooms lichen ruby rails
Language:Ruby 77
traitecoevo / fungaltraits
A dynamic database of fungal trait measurements
fungi database traits
Language:R 68
nextgenusfs / amptk
AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
amplicons microbiome mycobiome next-generation-sequencing fungi rdna coi lsu co1 mtco1
Language:Python 35
steineggerlab / ufcg
UFCG: Universal Fungal Core Genes
bioinformatics fungi genomics marker-gene-analysis phylogenetics
Language:Java 30
guyleonard / get_jgi_genomes
A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.
fungi jgi genomes genome protein-sequences mycocosm phytozome algae archaeplastida metazome jgi-genomes
Language:Perl 27
JTFouquier / ghost-tree
creating hybrid-gene phylogenetic trees for diversity analyses
python python3 phylogenetics phylogenetic-trees diversity fungi fungal microbiome microbiology microbial-ecology bioinformatics
Language:Python 27
JanaSperschneider / EffectorP-3.0
Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes
fungi oomycetes effector effectorp prediction cytoplasmic-effectors apoplastic-effectors
Language:Python 16
DEMENT-Model / DEMENTpy
A spatially explicit trait- and individual-based microbial systems modelling framework
dement trait microorganism bacteria fungi individual-based-modelling enzyme ecology community-ecology soil biology dementpy trait-based-modelling litter decomposition tradeoff microbiome fungus genome omics
Language:Python 13
domingoclub / fermenter-software
Domingo Fermenter software source code
fermentation mycelium tempeh koji fungi
Language:Python 13
Otoliths / SP2000
🐟Catalogue of Life toolkit for R
species2000 china biodiversity animals plants fungi microorganisms catalogue-of-life-china catalogue-of-life-global-checklist catalogue-of-life-taiwan-checklist redlist-of-chinese-biodiversity china-animal-scientific-database
Language:R 12
cparsania / FungiExpresZ
An R-shiny package to analyse and visualise fungal gene expression data
datavisualization fungi geneexpression rpackage shinyapp sra-data visualization visualizations
Language:R 9
obophenotype / fungal-anatomy-ontology
A structured controlled vocabulary for the anatomy of fungi
fungi obofoundry anatomy ontology anatomy-ontology
Language:Makefile 9
eslam-nasser / eslam-nasser.github.io
Interactive 3D fungi models built with Three.js
blender fungi interactive morphology threejs
Language:JavaScript 8
FusariumLifestyles
Rowena-h / FusariumLifestyles
Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085 🟣
bioinformatics comparative-genomics phylogenomics genome-assembly genome-annotation fungi
Language:R 8
Changwanseo / GenMine
GenBank Record downloader for taxonomists
fungi genbank taxonomy web-crawling
Language:Python 7
EverymanBio / pestalotiopsis
Assembly and phylogentic analysis pipeline for draft genome of a Pestalotiopsis fungi.
bioinformatics genomics genome-assembly nanopore phylogeny fungi pestalotiopsis ascomycete
Language:Python 7
akshayparopkari / RNAseq
Preprocessing and differential expression analysis for QuantSeq 3' mRNA-seq data
bash-script rna-seq preprocess differential-expression candida-albicans fungi sequence-alignment quality-control open-source visualization python3 r
Language:Shell 6
JanaSperschneider / EffectorP-2.0
Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0
fungal-effectors fungi effector-prediction
Language:Python 6
biocorecrg / microbiome_procedures
Mothur procedures for 16S and ITS analysis
microbiome-analysis microbiome-workflow 16s its mothur phyloseq fungi
Language:R 5
ccdmb / catastrophy
CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.
fungi bioinformatics trophic-interactions pathogenomics pathogen
Language:Python 5
Changwanseo / FunVIP
Fungal Identification Pipeline
fungi phylogenetic-tree species-delimitation species-identification taxonomy multigene
Language:Python 5
domingoclub / domingo-fermenter
A device to promote plant-based protein and open-source tools so that everyone can make them at home for the benefit of our lives and our planet
fermentation foodtech fungi microorganisms mycelium plant-proteins sustainability tempeh
5
mchiapello / Ramf
A package for arbuscular mycorrhyzal fungi colonization
r-package arbuscular mycorrhizal fungi colonization grid-system trouvelot
Language:R 5
Rowena-h / FungusNameCheck
A script to check fungus names for the most up to date nomenclature according to Species Fungorum 🍄
fungi taxonomic-classification
Language:R 5
vmikk / NextITS
A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
eukaryotes fungi internal-transcribed-spacer its metabarcoding nextflow pacbio pipeline
Language:Nextflow 5
Gardner-BinfLab / Razor
Tool to predict eukaryotic signal peptides. In addition, prediction of toxin and fungi signal peptides is also done.
signal-peptide cleavage-sites toxic-proteins fungi
Language:Python 4
amsesk / SCGid
SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries
bioinformatics-pipeline bioinformatics-algorithms bioinformatics-tool bioinformatics fungi eukaryotes single-cell-genomics genome-assembly-evaluation python3
Language:Python 3
MarufHasan24 / jsr
pre release of fungi language. Its a jsr version and documentation for fungi.
jsr programming-language fungi
Language:HTML 3
Rowena-h / GaeumannomycesGenomics
Scripts for Hill et al. (in review) 🌾
bioinformatics comparative-genomics fungi genome-annotation genome-assembly pangenomics phylogenetics phylogenomics
Language:R 3
Godrigos / mediadb
A small android application project listing commonly used microbiology culture media.
microbiology science fungi bacteria microalgae biology-lab-protocols
Language:Dart 2
onco-p53 / manuscripts
Code and data for my scientific publications
r bayesian phylogenetics manuscripts fungi bacteria chromista
Language:R 2
snewhouse / exotic-dna-ngs
WIP & POC: Count Viral and other non-human genome signatures in Human NGS data
ngs-pipeline ngs-analysis ngs genetics viral bacteria fungi clinical-research docker nextflow bash bioinformatics
Language:Shell 2
tylerhuyser / CanYouEatItFungusIdentificationApp
CAN YOU EAT IT is a web application that allows users to identify fungi by location & season.
fungi identify-fungi genus mushrooms mushroom-observer mushroom-classification
Language:JavaScript 2
fantin-mesny / amapec
Antimicrobial activity prediction for fungal effector candidates
annotation antimicrobial antimicrobial-peptides effector fungi machine-learning pdb-files prediction proteins structures
Language:Python 1
scoobyhax / taxonomy-browser-ncbi-fungi
Light weight NCBI taxonomy browser app made in Electron Fiddle
fungi genome
Language:JavaScript 1
SergioAlias / sporeflow
🦠 SporeFlow: Fungal ITS metataxonomics pipeline
fungi its pipeline qiime2 snakemake workflow metataxonomics
Language:Python 1

fungi

MushroomObserver / mushroom-observer

traitecoevo / fungaltraits

nextgenusfs / amptk

steineggerlab / ufcg

guyleonard / get_jgi_genomes

JTFouquier / ghost-tree

JanaSperschneider / EffectorP-3.0

DEMENT-Model / DEMENTpy

domingoclub / fermenter-software

Otoliths / SP2000

cparsania / FungiExpresZ

obophenotype / fungal-anatomy-ontology

eslam-nasser / eslam-nasser.github.io

Rowena-h / FusariumLifestyles

Changwanseo / GenMine

EverymanBio / pestalotiopsis

akshayparopkari / RNAseq

JanaSperschneider / EffectorP-2.0

biocorecrg / microbiome_procedures

ccdmb / catastrophy

Changwanseo / FunVIP

domingoclub / domingo-fermenter

mchiapello / Ramf

Rowena-h / FungusNameCheck

vmikk / NextITS

Gardner-BinfLab / Razor

amsesk / SCGid

MarufHasan24 / jsr

Rowena-h / GaeumannomycesGenomics

Godrigos / mediadb

onco-p53 / manuscripts

snewhouse / exotic-dna-ngs

tylerhuyser / CanYouEatItFungusIdentificationApp

fantin-mesny / amapec

scoobyhax / taxonomy-browser-ncbi-fungi

SergioAlias / sporeflow