Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: microbiome-analysis
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Language: MATLAB - Size: 1.02 GB - Last synced: about 8 hours ago - Pushed: about 8 hours ago - Stars: 237 - Forks: 302
adrianagiongo/RhizoWheat-ms1
Workflow and R scripts for Giongo et al. (2024)
Language: R - Size: 54.7 KB - Last synced: about 10 hours ago - Pushed: about 12 hours ago - Stars: 0 - Forks: 0
cafferychen777/MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Language: R - Size: 15.6 MB - Last synced: about 19 hours ago - Pushed: about 20 hours ago - Stars: 24 - Forks: 3
microbiome/microbiome
microbiome R package
Language: R - Size: 392 MB - Last synced: 2 days ago - Pushed: 9 months ago - Stars: 273 - Forks: 56
tmbuza/iMAP
iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline
Language: HTML - Size: 160 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 14 - Forks: 4
cafferychen777/MicrobiomeStat-Turtorial-Professional-Version
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
Size: 176 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 2 - Forks: 2
krisrs1128/mbtransfer
`mbtransfer` is an R package for modeling microbiome dynamics. It provides functions for fitting transfer function models, simulating counterfactual trajectories, and selecting significantly perturbed taxa using mirror statistics.
Language: R - Size: 37.3 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 2 - Forks: 0
AlexUmbach/AOViz
short-read amplicon data visualization suite
Language: R - Size: 11.5 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0
CMU-SAFARI/MetaTrinity
MetaTrinity is a novel metagenomic analysis tool employing efficient containment search techniques and heuristics for read mapping to achieve significant speedup while maintaining high accuracy. This positions MetaTrinity as an efficient solution, optimally balancing speed and precision in metagenomic analysis.
Language: HTML - Size: 53.3 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 4 - Forks: 1
YuLab-SMU/MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
Language: R - Size: 6.85 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 156 - Forks: 32
amnona/dbbact-calour
dbBact (https://dbbact.org) interface for Calour (https://github.com/biocore/calour) for microbiome 16S analysis
Language: Jupyter Notebook - Size: 132 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 1 - Forks: 0
david-barnett/microViz
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
Language: R - Size: 399 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 86 - Forks: 9
sablokgaurav/ontology-annotation-count
I implemented the arguably with a function to calculate the genome annotation for the microbiome and also for the other genomes. It will take a genome annotation or a text file and will prepare the count and also for the gene ontology analysis
Language: Python - Size: 25.4 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
waldronlab/curatedMetagenomicDataAnalyses
Analyses in R and Python Using curatedMetagenomicData
Language: Python - Size: 239 MB - Last synced: 2 days ago - Pushed: over 1 year ago - Stars: 19 - Forks: 5
Brochado-Kith/microbiome_analysis
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
Language: R - Size: 1.34 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0
CMU-SAFARI/Genome-on-Diet
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
Language: Roff - Size: 63 MB - Last synced: 3 days ago - Pushed: 7 months ago - Stars: 11 - Forks: 4
clemente-lab/mmeds-meta
A database for storing and analyzing omics data
Language: Python - Size: 890 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 2 - Forks: 1
m-crown/OMEinfo
Automated retrieval of consistent geographical metadata for microbiome research!
Language: Python - Size: 15.9 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 1
LebeerLab/tidytacos
Functions to manipulate and visualize microbial community data
Language: R - Size: 14.8 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 7 - Forks: 1
raeslab/dyspyosis
A python package to calculate the dysbiosis score in microbiome datasets
Language: Python - Size: 895 KB - Last synced: 21 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 0
GPZ-Bioinfo/tmap
topological data analysis of population-scale microbiomes
Language: Python - Size: 11.4 MB - Last synced: 8 days ago - Pushed: over 1 year ago - Stars: 30 - Forks: 10
TomC-93/Tree-Root-Microbiome-Project
The scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.
Language: HTML - Size: 1.63 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 1
sarahtanja/coral-pae-temp
This repo details the multi-stressor exposure experiment conducted in August 2022 at Hawaii Institute of Marine Biology (HIMB) in Kaneohe Bay. In this experiment coral fragments were exposed to increasing levels of phthalate pollution and thermal stress for 48 hours.
Language: Jupyter Notebook - Size: 1.21 GB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0
qiita-spots/qiita
Qiita - A multi-omics databasing effort
Language: Python - Size: 45.2 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 119 - Forks: 79
TessaBeaver/TBeaver-G-childressi-microbiome-analysis
Microbial community dynamics during key life-history transitions in the chemosymbiotic mussel, Gigantidas childressi
Language: R - Size: 13.7 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
cafferychen777/MicrobiomeStat-Shiny
A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.
Language: R - Size: 1.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 1
Weimar45/Andera
En este repositorio se crearán diferentes flujos de trabajo para el análisis del microbioma con Bioconductor.
Language: HTML - Size: 134 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
statdivlab/paramedic
Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations
Language: R - Size: 120 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 12 - Forks: 1
jordiabante/biodive
A reference-free statistical approach to diversity-generating & mobile genetic element discovery
Language: Python - Size: 959 KB - Last synced: 28 days ago - Pushed: about 1 year ago - Stars: 5 - Forks: 0
JelenaBanjac/microbiome-toolbox
Early Life Microbiome Toolbox
Language: Jupyter Notebook - Size: 67.9 MB - Last synced: 10 days ago - Pushed: 4 months ago - Stars: 8 - Forks: 2
mmpust/IPMN-repository
R session, R scripts, and additional resources accompanying the BMJ Gut paper
Language: R - Size: 424 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
microbiome/miaViz
Microbiome Analysis Plotting and Visualization
Language: R - Size: 1.24 GB - Last synced: about 11 hours ago - Pushed: about 12 hours ago - Stars: 7 - Forks: 8
ihdavjar/Data_For_Biomarker_Analysis
This Repo contains all the data required for Biomarker Analysis of gut cancer patients.
Language: R - Size: 12.6 MB - Last synced: 5 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0
mucosal-immunology-lab/microbiome-analysis
A selection of analytical approaches, tools, and utilities for the processing of microbiome data derived from either 16S rRNA amplicon sequencing or shotgun metagenomics.
Language: R - Size: 1.6 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0
cepdnaclk/e17-6sp-Host-Pathogen-Interaction
Building the software for analyzing the microbiome data using machine learning technics. the application provides the GUI for the user they can easily analyze the data without any other programming knowledge developed by @piriyaraj @varnaraj @thanujan @rilwan292
Language: CSS - Size: 29.2 MB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 5
ImPaisley/TaxaAbundance_Test
Outlines the process of testing for statistical differences in certain taxa by group utilizing the phyloseq, tidyverse, and various statistical packages within R.
Language: R - Size: 2.93 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0
yiluheihei/shiny-RevEcoR
An interactive web application that provides a flexible graphical user interface (GUI) to the Reverse Ecology analysis package for R
Language: R - Size: 20.7 MB - Last synced: 6 months ago - Pushed: about 8 years ago - Stars: 3 - Forks: 0
niaid/microbiome
Microbiome Data Analysis and Nephele Demo
Size: 14.6 KB - Last synced: 6 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 1
mikemc/metacal
Metagenomics calibration R package
Language: R - Size: 1.63 MB - Last synced: 6 months ago - Pushed: about 2 years ago - Stars: 17 - Forks: 4
microsud/Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Language: CSS - Size: 6.07 MB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 100 - Forks: 45
meyermicrobiolab/Stony-Coral-Tissue-Loss-Disease-SCTLD-Project
R scripts used for the analysis of microbiomes associated with stony coral tissue loss disease (SCTLD) in the Florida Reef Tract
Language: R - Size: 1.93 GB - Last synced: 6 months ago - Pushed: over 4 years ago - Stars: 4 - Forks: 0
cb-42/cbmbtools
General purpose package containing useful functions for microbiome analysis pipelines
Language: R - Size: 165 KB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1
carden24/V-Xtractor
Repository for V-Xtractor an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences
Language: Perl - Size: 1.08 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 5 - Forks: 2
zoecastillo/microbiomeExplorer
The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.
Language: R - Size: 1.82 MB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 66 - Forks: 21
jjcolgan/group7Repo
Predictive model, utilizes several machine learning algorithms to predict patient disease status from abundance data
Language: Python - Size: 233 KB - Last synced: 6 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 2
nthomasCUBE/microbComp
pairwise comparison between two OTU - species abundance tables
Language: R - Size: 174 KB - Last synced: 6 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 1
grimmlab/MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Language: Shell - Size: 13.6 MB - Last synced: 6 months ago - Pushed: about 2 years ago - Stars: 89 - Forks: 34
Russel88/MicEco
Various functions for analysis of microbial community data
Language: R - Size: 873 KB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 36 - Forks: 11
DenisAShah/ZIDM Fork of mkoslovsky/ZIDM
Code for Matt Koslovsky's paper
Size: 451 KB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
DenisAShah/Frontiers_2017 Fork of ggloor/Frontiers_2017
Supplement for Frontiers article
Size: 1.19 MB - Last synced: 8 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0
hhuang2018/mwas Fork of danknights/mwas
Generic code for performing microbiome-wide association studies with a variety of models
Language: R - Size: 4.25 MB - Last synced: 8 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0
jtremblay/microbiomeutils
Python utility to generate distance matrices, perform PCoAs and generate taxonomic summaries using simple tab-separated feature tables.
Language: Python - Size: 275 KB - Last synced: 8 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
jessmhoehner/Methods Fork of EmoryIntegratedComputationalCore/Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
Language: R - Size: 18 MB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
smdabdoub/phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Language: Python - Size: 79.7 MB - Last synced: 27 days ago - Pushed: over 2 years ago - Stars: 12 - Forks: 4
microsud/microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Language: R - Size: 40 MB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 31 - Forks: 6
TealFurnholm/Strain-Level_Metagenome_Analysis
Using a universal reference database, mixed assemblies, and cutting-edge software to give you the quantitative community phylogeny, a complete community functional analysis, and many strain(ish)-level high-quality bins.
Language: Perl - Size: 821 KB - Last synced: 6 months ago - Pushed: about 2 years ago - Stars: 3 - Forks: 2
ahmedmoustafa/ALS
Analysis of the gut microbiome of Amyotrophic Lateral Sclerosis (ALS) patients using the DADA2 workflow
Language: Jupyter Notebook - Size: 3.62 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
sroitman/Varadero_coral_microbiome
All code and analyses performed for: Roitman, S., López-Londoño, T., Joseph Pollock, F. et al. Surviving marginalized reefs: assessing the implications of the microbiome on coral physiology and survivorship. Coral Reefs 39, 795–807 (2020).
Size: 8.39 MB - Last synced: 9 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0
LeonDlugosch/MetaSeq-Toolkit
This pipeline is intended to be a convenient way to work though large sets of metagenomic or metatranscriptiomic datasets while also retaining high analytical flexibility due to retained intermediate results that might be useful outside of the intended purpose.
Language: Shell - Size: 102 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1
microsud/microbiometutorials.gihub.io
This website gives an introduction to microbial community analysis.
Language: HTML - Size: 6.04 MB - Last synced: 9 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0
Amit-H/Mining-for-microbes
Reusing publicly available whole transcriptome data to determine the state of the microbiome at time of sampling.
Size: 1000 Bytes - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
vllorens/benchmark_microbiome_transformations
Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"
Language: R - Size: 45.1 MB - Last synced: 9 months ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 4
FabbriniMarco/microbAIDeR
An ensemble of functions for easier and quicker preliminary microbiome analyses
Language: R - Size: 232 KB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0
joycewang914/Nursing_Home_Patient_Gut_Microbiota
Identifying gut microbiome features associated with the risk of acquiring an enteric drug-resistant organism (e.g. vancomycin-resistant Enterococcus and resistant gram-negative bacteria) in patients recently discharged from acute-care hospital and admitted into nursing homes.
Language: R - Size: 207 KB - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0
SevanEsaian/Giant-Kelp-Associated-Microbiome-Metagenomics
This repository contains bash scripts, R code, and explanations for the steps involved in assembling and analyzing the metagenomes of bacteria from giant kelp blades in the Santa Barbara Channel.
Size: 23.4 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
RiboRings/mia_presentations
quarto presentations about microbiome analysis and data integration
Language: JavaScript - Size: 2.45 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
sPuntinG/Galaxea_Microbiome_PCI
Code and raw data for *Galaxea fascicularis* microbiome data analysis
Language: R - Size: 11.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0
vanessapino/AUMicrobio
AU microbiome molecular exploratory analyses for NSW
Language: R - Size: 17.6 KB - Last synced: 3 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
garudlab/Signature-SNVs
Signature-SNVs a method for selecting signature SNVs from metagenomic data for input into FEAST for source tracking.
Language: R - Size: 1.74 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 2 - Forks: 0
wijerasa/bioinformatics-projects
A Collection of Bioinformatics Projects
Language: Python - Size: 9.2 MB - Last synced: 9 months ago - Pushed: over 5 years ago - Stars: 7 - Forks: 4
yanxianl/Li_AqFl1-Microbiota_2021
Code for reproducing results published in the paper: "Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets"
Language: HTML - Size: 450 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 1
dib-lab/2021-paper-ibd
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease
Language: HTML - Size: 44.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 3
rajaldebnath/Code-documentation
Project code documentation
Language: Jupyter Notebook - Size: 530 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
bioinfonupeb/hfd-insitu-microbiome
Codes for the statistical analysis that investigates the impact of high-fat diet on gut microbiome and serotonergic gene expression in the raphe nuclei.
Language: Shell - Size: 28.3 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0
val92loz/HFD-NR_microbiome
This repository provides the scripts used to analyze the metagenomics data from the paper Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice.
Language: Python - Size: 215 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
gerverska/fun-gi
hamPCR + Douglas-fir + needle fungi
Language: HTML - Size: 96.3 MB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
Zubair2021/16S_Microbiome_Analysis
This repository provides scripts for the 16S microbiome analysis and metagenome prediction using linux and R-Studio
Language: Shell - Size: 33.2 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 1
rwst/process-ubiome-16S 📦
process raw reads from ubiome
Language: Python - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0
RIVM-IIV-Microbiome/biomeUtils
biomeUtils is Module-01 of the RIVM-ToolBox. R pkg with common utilities for microbiome research done at the RIVM.
Language: R - Size: 4.9 MB - Last synced: 8 months ago - Pushed: 10 months ago - Stars: 3 - Forks: 0
vallenderlab/MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
Language: R - Size: 18.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 18 - Forks: 3
YushuShi/sparseMbClust
Use MFMDM and MFMDTM to cluster microbiome data
Language: MATLAB - Size: 992 KB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1
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
valentynbez/spatial_sinus_microbiome
Code for the paper "Spatial variability of the microbiome in chronic rhinosinusitis is associated with the patients’ clinical characteristics but not with sinus ostia occlusion" by Szaleniec et al. 2022
Language: Jupyter Notebook - Size: 4.42 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 1
RiboRings/uranouchi42microdiversity
In this repository live the bash, R and Julia scripts used to explore the microdiversity of the prokaryotic community at Uranouchi Inlet (42-sample time-series) by means of metagenomic shotgun sequencing under the supervision of the Ogata Lab.
Language: R - Size: 110 KB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
RiboRings/uranouchi9microdiversity
In this repository live the bash, R and Julia scripts used to explore the microdiversity of the prokaryotic community at Uranouchi Inlet (9-sample time-series) by means of metagenomic shotgun sequencing under the supervision of the Ogata Lab.
Language: R - Size: 50.8 KB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
niaid/metagenote-training
Training materials for METAGENOTE
Size: 6.69 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1
shivankurkapoor/microbiome-data-analysis
Microbiome Data Analysis
Language: Python - Size: 42 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0
Djeppschmidt/QSeq
QSeq package and functions for microbiome analysis
Language: R - Size: 85.9 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0
marinavannucci/dmbvs Fork of duncanwadsworth/dmbvs
R/C code for Bayesian variable selection for Dirichlet-multinomial regression models. Accompany paper: Wadsworth et al. (2016). An Integrative Bayesian Dirichlet-Multinomial Regression Model for the Analysis of Taxonomic Abundances in Microbiome data. BMC Bioinformatics 18:94.
Language: C - Size: 214 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 1
BioSina/STARA
A general 16S rDNA sequencing analysis pipeline
Language: Python - Size: 26.4 KB - Last synced: 11 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
guokai8/microbial
Do microbiome analysis with dada2 and phyloseq object
Language: R - Size: 859 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 8 - Forks: 2
northomics/pepFunk
Peptide-centric functional enrichment tool
Language: R - Size: 18.5 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 4 - Forks: 2
EmoryIntegratedComputationalCore/Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
Language: R - Size: 18 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 5 - Forks: 2
pnnl/brislawn-2018-founders-species
🦠 📓 a microbiome paper
Language: HTML - Size: 11 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 6 - Forks: 1
knightlab-analyses/dynamics
Analysis of Multiple Circadian/Longitudinal Datasets
Language: Jupyter Notebook - Size: 43.6 MB - Last synced: 12 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0
DanielSprockett/reltools
Microbiome Amplicon Analysis and Visualization
Language: R - Size: 32.2 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 5 - Forks: 0
erictleung/dada2HPCPipe
:ocean: 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM
Language: R - Size: 92.8 KB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 3 - Forks: 2
FischbachLab/hCom_variable_regions
Extract and compare variable regions from hCom genomes.
Language: Shell - Size: 18.6 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0
AlmaasLab/micInt
R package for analyzing microbial co-occurences
Language: R - Size: 747 KB - Last synced: 6 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0
chuanfuyap/motu-python-package
Tools to handle metagenomic data manipulation
Language: Python - Size: 56.6 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0