Changwanseo/FunVIP

Fungal Identification Pipeline

Language: Python - Size: 117 MB - Last synced: about 1 hour ago - Pushed: about 2 hours ago - Stars: 5 - Forks: 0

vmikk/NextITS

A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio

Language: Nextflow - Size: 2.34 MB - Last synced: about 9 hours ago - Pushed: about 22 hours ago - Stars: 5 - Forks: 0

amsesk/SCGid

SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries

Language: Python - Size: 11 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 3

steineggerlab/ufcg

UFCG: Universal Fungal Core Genes

Language: Java - Size: 71.1 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 26 - Forks: 0

mrdbidwill/mrdbid-p

mrdbid-p is the php mysql version of mrdbid.com - not assured of any future development

Language: PHP - Size: 133 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0

bioatmosphere/TAM

Taming Fine-root Systems Complexity with TAM(Transport and Absorptive fine roots with Mycorrhizal funig) in ecosystem and biosphere modelling

Language: Jupyter Notebook - Size: 20.8 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 1 - Forks: 0

Jason-Zen/Fungal_Taxonomy

Programs for fungal taxonomic studies

Language: Python - Size: 208 KB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 0 - Forks: 0

esovm/CCBI Fork of Deewiant/CCBI

The Conforming Concurrent Befunge–98 Interpreter.

Size: 1.15 MB - Last synced: 30 days ago - Pushed: over 12 years ago - Stars: 0 - Forks: 0

MushroomObserver/mushroom-observer

A website for sharing observations of mushrooms.

Language: Ruby - Size: 84.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 75 - Forks: 26

Godrigos/mediadb

A small android application project listing commonly used microbiology culture media.

Language: Dart - Size: 1.88 MB - Last synced: 15 days ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

stajichlab/stajichlab.github.io Fork of greenelab/lab-website-template

Stajich Lab Website

Language: HTML - Size: 437 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 3

guyleonard/get_jgi_genomes

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

Language: Perl - Size: 86.9 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 27 - Forks: 5

cparsania/FungiExpresZ

An R-shiny package to analyse and visualise fungal gene expression data

Language: R - Size: 335 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 9 - Forks: 0

Otoliths/SP2000

🐟Catalogue of Life toolkit for R

Language: R - Size: 904 KB - Last synced: 16 days ago - Pushed: 6 months ago - Stars: 12 - Forks: 3

Rowena-h/GaeumannomycesGenomics

Scripts for Hill et al. (in prep) 🌾

Language: R - Size: 3.08 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

ccdmb/catastrophy

CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.

Language: Python - Size: 2.08 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0

aldendirks/amf_metabarcoding

Public repository of data and analyses from Dirks and Jackson (2020), "Community structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy", Applied and Environmental Microbiology 86 (19)

Language: R - Size: 58.2 MB - Last synced: 3 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

domingoclub/fermenter-software

Domingo Fermenter software source code

Language: Python - Size: 676 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 11 - Forks: 2

DEMENT-Model/DEMENTpy

A spatially explicit trait- and individual-based microbial systems modelling framework

Language: Python - Size: 29.3 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 13 - Forks: 4

traitecoevo/fungaltraits

A dynamic database of fungal trait measurements

Language: R - Size: 2.88 MB - Last synced: 4 months ago - Pushed: about 4 years ago - Stars: 63 - Forks: 9

nextgenusfs/amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

Language: Python - Size: 18.3 MB - Last synced: 27 days ago - Pushed: 6 months ago - Stars: 35 - Forks: 14

fantin-mesny/amapec

Antimicrobial activity prediction for fungal effector candidates

Language: Python - Size: 19.2 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

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

Size: 758 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 6 - Forks: 0

gnick18/Fungal_ICSBGCs

Reproducible code and data repository for the fungal ICS BGC prediction publication. GitHub repository is managed by Grant Nickles. For any data related questions email [email protected] or [email protected]. For publication questions reach out to the corresponding authors Dr. Drott at [email protected] or Dr. Keller at [email protected].

Language: HTML - Size: 196 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

UU-Microbial-Eukaryotes/ebook

An e-book about the evolution and diversity of microbial eukaryotes including fungi.

Language: SCSS - Size: 103 MB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

kblin/fungal-ui

A web UI for the fungal version of antiSMASH.

Language: JavaScript - Size: 540 KB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

JanaSperschneider/EffectorP-3.0

Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes

Language: Python - Size: 67.6 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 10 - Forks: 4

JanaSperschneider/EffectorP-2.0

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

Language: Python - Size: 147 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 6 - Forks: 6

GSMc-Fungi/GSMc-Fungi.github.io

The Global Soil Mycobiome consortium dataset

Size: 1.12 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 1

mrdbidwill/www

Stores mushroom observation data

Language: PHP - Size: 158 MB - Last synced: 8 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

obophenotype/fungal-anatomy-ontology

A structured controlled vocabulary for the anatomy of fungi

Language: Makefile - Size: 174 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 8 - Forks: 3

PerisD/EukCCC1

Alignments and trees from the Sorribes et al Review about CCC1

Size: 328 KB - Last synced: 9 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

PerisD/TriMAT

Assemblies, MATA/MATB regions and source data from Peris et al 2022

Language: Python - Size: 8.77 MB - Last synced: 9 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

MarufHasan24/jsr

pre release of fungi language. Its a jsr version and documentation for fungi.

Language: HTML - Size: 85.9 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 0

ruidovacio/toxic-shroom-api

An API for accessing a database of toxic mushrooms

Language: HTML - Size: 660 KB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

Gardner-BinfLab/Razor

Tool to predict eukaryotic signal peptides. In addition, prediction of toxin and fungi signal peptides is also done.

Language: Python - Size: 30.3 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 1

EverymanBio/pestalotiopsis

Assembly and phylogentic analysis pipeline for draft genome of a Pestalotiopsis fungi.

Language: Python - Size: 205 KB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 7 - Forks: 2

helvm/Funge-98 Fork of catseye/Funge-98

The Funge-98 specification in all its gory

Size: 92.8 KB - Last synced: 22 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

helvm/fungi Fork of thomaseding/fungi

Funge-98 interpreter and debugger written in Haskell

Size: 113 KB - Last synced: 22 days ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

scoobyhax/taxonomy-browser-ncbi-fungi

Light weight NCBI taxonomy browser app made in Electron Fiddle

Language: JavaScript - Size: 265 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

TCZ-FP-RandD/CryoManuscript

Publicly avalible data for "Fungal cryopreservation across 61 genera: Practical application and method evaluation" (manuscript publication pending review).

Language: R - Size: 195 KB - Last synced: 4 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

vanessapino/AUMicrobio

AU microbiome molecular exploratory analyses for NSW

Language: R - Size: 17.6 KB - Last synced: 4 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

JTFouquier/ghost-tree

creating hybrid-gene phylogenetic trees for diversity analyses

Language: Python - Size: 18.5 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 26 - Forks: 19

Rowena-h/MusaEndophytes

Script and data for Hill et al. (2021) doi: 10.3389/fmicb.2021.643731 🍌

Language: R - Size: 5.2 MB - Last synced: 4 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 1

Rowena-h/FusariumLifestyles

Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085

Language: R - Size: 19.4 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 3 - Forks: 3

Rowena-h/AscomycotaGapAnalysis

Script and data for Hill, Leitch & Gaya (2021) doi: 10.1016/j.fbr.2021.03.003

Language: R - Size: 2.31 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

Rowena-h/EndophyteGenomes

Scripts for Hill et al. (2023) doi:10.1093/gbe/evad038

Language: Shell - Size: 2.68 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

Brookesloci/fungi_intron_paper_2020

Language: Jupyter Notebook - Size: 874 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

jsolorzano734/Xylaria_necrophoraSMs

Repository containing data and code for analyses for the Xylaria necrophora Secondary Metabolites

Language: R - Size: 192 KB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

TraxlerLab/RNAseq_2021Pyonema

Code associated with Fischer, et al (2021) "Pyrolyzed Substrates Induce Aromatic Compound Metabolism in the Post-fire Fungus, Pyronema domesticum"

Size: 7.81 KB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

gerverska/fun-gi

hamPCR + Douglas-fir + needle fungi

Language: HTML - Size: 96.3 MB - Last synced: 22 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

Changwanseo/GenMine

GenBank Record downloader for taxonomists

Language: Python - Size: 178 KB - Last synced: about 10 hours ago - Pushed: 8 days ago - Stars: 7 - Forks: 0

tylerhuyser/CanYouEatItFungusIdentificationApp

CAN YOU EAT IT is a web application that allows users to identify fungi by location & season.

Language: JavaScript - Size: 89.4 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

Next-ITS/next-its.github.io

NextITS pipeline documentation

Size: 7.55 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

johannessonlab/Letharia

All scripts and pipelines related to inferring ploidy, hybridization and MAT locus architecture in the lichen symbionts from the genus Letharia

Language: R - Size: 16.7 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

onco-p53/manuscripts

Code and data for my scientific publications

Language: R - Size: 919 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

julsfreedman/Mod-1-DOM-Based-Game

Shroomemory

Language: JavaScript - Size: 525 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

lindaicing/shroombase

Mushroom Catalog

Language: HTML - Size: 236 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

biocorecrg/microbiome_procedures

Mothur procedures for 16S and ITS analysis

Language: R - Size: 124 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 3 - Forks: 6

guyleonard/blastocladiella

The genome of Blastocladiella emersonii

Language: HTML - Size: 110 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

Rowena-h/FungusNameCheck

A script to check fungus names for the most up to date nomenclature according to Species Fungorum

Language: R - Size: 25.4 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

eslam-nasser/eslam-nasser.github.io

Interactive 3D fungi models built with Three.js

Language: JavaScript - Size: 54 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 8 - Forks: 1

akshayparopkari/RNAseq

Preprocessing and differential expression analysis for QuantSeq 3' mRNA-seq data

Language: Shell - Size: 73.2 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0

mchiapello/Ramf

A package for arbuscular mycorrhyzal fungi colonization

Language: R - Size: 10.5 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 4 - Forks: 2

hjsimpso/fungarium_book

A guide to using fungarium for comprehensive analyses of ecological traits in fungi.

Language: TeX - Size: 10.2 MB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

hjsimpso/fungarium

An R package for enabling the use of fungarium collection data in comprehensive trait analyses.

Language: R - Size: 22.4 MB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

sghosh89/CMN

Explore model for coexistence of beneficial and non-beneficial symbionts for plants

Language: R - Size: 163 MB - Last synced: 12 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

BehnsenLab/Siderophores

Xenosiderophores produced by gut commensal fungi or present in the diet promote Salmonella enterica serovar Typhimurium growth and gut colonization

Language: R - Size: 236 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

herptilemicrobiomes/herptilemicrobiomes.github.io

Herptile MIcrobiomes Project

Language: SCSS - Size: 24 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 1

dagahren/dagahren.github.io

Ahren Lab page

Size: 29.5 MB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

zygolife/zygolife.github.io-old

Zygolife website

Size: 1000 Bytes - Last synced: 4 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

CALeDNA/POUR

Size: 40.6 MB - Last synced: 4 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

SLAment/Podosporaceae

A small pipeline to analyse marker data into a phylogeny

Language: Python - Size: 190 KB - Last synced: 4 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

Ld-monkey/DOWNLOAD_JGI_GENOMES

Script python permettant de télécharger les séquences de la base de donnée JGI.

Language: Python - Size: 12.7 KB - Last synced: 12 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

sethiyap/Cg_oxidative_stress

Oxidative stress response of Candida glabrata.

Language: HTML - Size: 8.98 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

gaberosenfield/Glass-Lab-Flow-Cytometry-Analysis

Contains MATLAB scripts used by members of the Glass Lab at UC Berkeley to analyze flow cytometry data.

Language: MATLAB - Size: 4.37 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

stajichlab/Afum_EVOL20

Identification of SNPs in EVOL20 strain of A. fumigatus

Language: Shell - Size: 13.1 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

terrimporter/MahmoudiEtAl2013

Code that was used to generate figures for the Mahmoudi et al., 2013 publication

Language: R - Size: 9.77 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

guyleonard/genome_crossovers

Which genomes are where in the big DBs?

Language: R - Size: 165 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

maxemil/Biodiversity-pipeline

Pipeline to characterize and analyse fungal microbiomes

Language: Groovy - Size: 626 KB - Last synced: 4 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

snewhouse/exotic-dna-ngs

WIP & POC: Count Viral and other non-human genome signatures in Human NGS data

Language: Shell - Size: 114 KB - Last synced: 7 months ago - Pushed: almost 7 years ago - Stars: 2 - Forks: 0

alskipp/Mycorec

Haskell fungus parsing 🍄

Language: Haskell - Size: 30.3 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0