Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: microbial-ecology
KasperSkytte/ampvis2
Tools for visualising microbial community amplicon data
Language: R - Size: 134 MB - Last synced: about 8 hours ago - Pushed: about 21 hours ago - Stars: 64 - Forks: 23
npechl/empclima
Microbial co-occurrence network reveals climate and geographic patterns for soil diversity on the planet
Language: R - Size: 26.9 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0
pyubero/microguilds
Pipepline for the standard quantification of microbial guilds from metagenomic samples.
Language: Jupyter Notebook - Size: 53.3 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 2 - Forks: 0
tklammsteiner/tklammsteiner.github.io
Personal website
Language: JavaScript - Size: 216 MB - Last synced: 23 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0
sipbs-compbiol/BM211-workshops
BM211 workshop materials
Language: TeX - Size: 155 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0
orphanlab/DeepSee
Visualize deep ocean biogeochemical sediment samples in 2D and 3D
Language: Vue - Size: 63.3 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0
pchlenski/misdeed
Microbiome data simulator for power analysis
Language: Jupyter Notebook - Size: 23.5 MB - Last synced: 3 months ago - Pushed: 7 months ago - Stars: 5 - Forks: 1
franciscozorrilla/metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Language: Python - Size: 262 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 160 - Forks: 34
bglarkin/tallgrass_restoration_legacies
Agricultural practices in cropland, like soil tillage and fertilizer applications, profoundly alter soil physical and chemical properties over time.
Language: R - Size: 103 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0
Gibbons-Lab/isb_course_2023
Materials and presentation for the 2023 ISB Microbiome course.
Language: Jupyter Notebook - Size: 245 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 15 - Forks: 7
mooreryan/iroki
Super snazzy online phylogenetic tree viewer with automatic customization using simple, tab-separated text files.
Language: HTML - Size: 15.6 MB - Last synced: 22 days ago - Pushed: about 1 year ago - Stars: 28 - Forks: 1
tklammsteiner/fromwastetofeed
From Waste to Feed | Insect Biotech Research Group
Language: JavaScript - Size: 38.5 MB - Last synced: 23 days ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
Gibbons-Lab/isb_course_2022
Materials and presentation for the 2022 ISB Microbiome course.
Language: Jupyter Notebook - Size: 258 MB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 23 - Forks: 8
Headonpillow/16S_analysis
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
Language: R - Size: 70.3 KB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0
lab42open-team/pubmed_trend_analysis
PubMed trend analysis of ecological keywords
Language: R - Size: 17.4 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0
singuyenmai/RLMicroInfect_poly-infect
Suppressing bacteria in microbial communities with reinforcement learning
Language: Jupyter Notebook - Size: 1.58 GB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0
lch14forever/beem-static
📦BEEM-Static: An R package for inferring microbial interactions based on Lotka-Volterra models
Language: R - Size: 5.15 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 8
anwarMZ/CoMW
Comparative Metatranscriptomics Workflow
Language: Python - Size: 175 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 6 - Forks: 3
GenomicaMicrob/chimera_detector
A simple script to detect chimeric sequences in 16S/18S metagenomic samples.
Size: 16.6 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
GenomicaMicrob/mg_classifier
Super fast script for classifying metagenomic 16S/18S sequences
Language: Perl - Size: 1.25 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
GenomicaMicrob/metagenomic_pipeline
Description of the metagenomic pipeline we have for analysis of 16S and 18S amplicon NGS
Size: 9.77 KB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 1
Russel88/MicEco
Various functions for analysis of microbial community data
Language: R - Size: 873 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 36 - Forks: 11
rrohwer/limony
lake itag measurements over nineteen years
Language: R - Size: 41.6 MB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 4 - Forks: 0
FAIR-MI/miiid-schema
A metadata schema for the Minimum Information about Intermicrobial Interaction Data (MIIID) using LinkML
Language: Python - Size: 715 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 2 - Forks: 0
alejandrorgijon/a_genomic_perspective_2022
Sup. Table 1 from RodrÃguez-Gijón and Nuy et al., 2022 (Front. in Microbiology)
Size: 6.66 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
karkman/Physalia_EnvMetagenomics_2023
Environmental metagenomics, Spring 2023, Physalia Courses
Size: 32.7 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 4 - Forks: 1
DanielSprockett/danielsprockett.github.io
My personal research website
Language: HTML - Size: 45.8 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 2 - Forks: 0
juanvillada/Microbial-Consortia-Dynamics-R
Modeling the dynamics of microbial communities (ODEs)
Language: R - Size: 586 KB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
Robaina/MetaTag
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
Language: Python - Size: 70.3 MB - Last synced: 12 months ago - Pushed: 12 months 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
karkman/Physalia_EnvMetagenomics_2022
Environmental metagenomics, Spring 2022, Physalia Courses
Language: R - Size: 79.8 MB - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 5 - Forks: 3
cpauvert/mi-atlas
Interactive and evolving catalogue of microbial interactions based on the framework of Pacheco and Segrè (2019)
Language: R - Size: 278 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
dizak/mothulity
Easy-to-use tool facilitating work with Mothur.
Language: JavaScript - Size: 29.3 MB - Last synced: 25 days ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 3
NewtonLabUWM/Sewage_TimeSeries
Data and code for LaMartina et al., 2021
Language: R - Size: 26.8 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 2 - Forks: 1
bioatmosphere/microbiome-climate-gradient
Application of DEMENTpy to a climate gradient in Southern California
Language: Jupyter Notebook - Size: 232 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1
kenscripts/duckweed_microbiome
QIIME 2 and R code along with manifests, metadata, inputs, and outputs for duckweed microbiome project (Acosta et al, 2020, Plos One).
Language: R - Size: 76.5 MB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
LLNL/2022_DVRFS_microbiome
Scripts for a manuscript titled "Subsurface Microbial Communities Reflect Regional-Scale Groundwater Hydraulic Connectivity" (submitted)
Language: R - Size: 61.5 KB - Last synced: 29 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 2
loulanomics/Full16S_sewageDatabase
Full-length bacterial 16S rRNA marker genes from a diverse wastewater sample set. LaMartina, et al., ASM Resource Announcement, 2022
Language: R - Size: 7.44 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 2
mmpust/airway-metagenome-infants
R scripts, metadata, input files & reference database
Size: 464 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0
TamayoLeivaJ/Dataviz_Stats_R_ES
Taller introductorio orientado a la visualización, análisis estadÃstico y ecológico en R, dirigido al manejo de datos en investigación, e impartido para la PUC durante 2021.
Language: HTML - Size: 92.6 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0
NewtonLabUWM/DrinkingWaterPipe_Ecology
Data and code for Kimbell et al., 2021
Language: R - Size: 3.42 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1
alexmanuele/QUOREM Fork of mwhall/QUOREM
QUOR'EM: Query, Update, Organize, and Render 'EM
Language: HTML - Size: 82.8 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
carpentries-incubator/eukref_pr2
EukRef PR2
Language: Python - Size: 2.34 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0
ryansmcgee/pycrobe
A simple package for simulations of microbial growth experiments with realistic sources of error.
Language: Python - Size: 247 KB - Last synced: 2 days ago - Pushed: about 4 years ago - Stars: 2 - Forks: 2
smjacques/thirsty_bromeliad
Data from ecological studies about how the climate change drives the microbial community dinamycs in aquatic ecosystems
Language: HTML - Size: 16.7 MB - Last synced: 2 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
