Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: dada2

Repositories

aomlomics/tourmaline

Amplicon sequence processing workflow using QIIME 2 and Snakemake

Language: Python - Size: 48.2 MB - Last synced: about 8 hours ago - Pushed: about 9 hours ago - Stars: 37 - Forks: 18

sebrauschert/OceanOmics-amplicon

A pipeline to analyse marine fish amplicon data

Language: R - Size: 42.2 MB - Last synced: 1 day ago - Pushed: 9 months ago - Stars: 4 - Forks: 2

cafferychen777/MicrobiomeStat

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

Language: R - Size: 15.7 MB - Last synced: about 7 hours ago - Pushed: 2 days ago - Stars: 24 - Forks: 3

IMCBioinformatics/dada2_snakemake_workflow

Amplicon sequencing workflow with snakemake and dada2

Language: R - Size: 972 KB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 2 - Forks: 1

jdmagasin/nifH-ASV-workflow

Workflow stages and data for Morando, Magasin et al. 2024

Language: R - Size: 23.2 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0

xuan13hao/data_analysis

Bioinformatic data analysis scripts and pipelines

Language: Jupyter Notebook - Size: 43.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

claraqin/neonMicrobe

Processing NEON soil microbe marker gene sequence data into ASV tables.

Language: R - Size: 958 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 2

ycl6/dada2 Fork of benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

Language: R - Size: 465 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

SevanEsaian/16S-Preparation-and-Analysis-Workflow

The purpose of this repository is to store R scripts that were used for 16S community compositional analyses.

Language: R - Size: 65.4 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

quadram-institute-bioscience/dadaist2

Dadaist2 🟨 Highway to R

Language: HTML - Size: 39.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 13 - Forks: 5

DavideScarpetta/taxonomic_profiling

Metabarcoding analysis pipeline, using DADA2 and qiime2

Language: Shell - Size: 65.4 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

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

adriaaula/dada2_guidelines

A repository with a general dada2 pipeline for amplicon processing

Language: R - Size: 80.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 8 - Forks: 3

ycl6/16S-rDNA-V3-V4

16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

Language: R - Size: 309 KB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 27 - Forks: 17

shandley/Microbiome-Analysis-Using-R

Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

Language: HTML - Size: 32.4 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 22 - Forks: 23

RemiMaglione/r-scripts

all my dirty r-scripts

Language: R - Size: 208 KB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 4 - Forks: 3

jjcolgan/Bodke-Script

Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2

Size: 3.91 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

En este repositorio se encuentran todos los scripts utilizados para mi tesis de licenciatura, titulada: "Análisis de perfiles funcionales de la microbiota intestinal de pacientes con trastorno depresivo mayor", la cual utiliza un lenguaje de programación en R y Phyton.

Language: R - Size: 634 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

microUCPH/amplicon_data_analysis

Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project

Language: HTML - Size: 8.23 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 10 - Forks: 6

leholman/metabarTOAD

A metabarcoding pipeline for analysing Illumina amplicon data.

Language: HTML - Size: 4.95 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 5 - Forks: 1

danote/Samail_16S_compilation

Processing of 16S rRNA gene amplicon sequences from from Samail Ophiolite, Oman

Language: R - Size: 36.3 MB - Last synced: 9 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

jdmagasin/nifH_amplicons_DADA2

DADA2 pipeline for nitrogenase (nifH) amplicon sequences (Illumina paired-end)

Language: R - Size: 34.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

NineFR09/Frontiers-10.3389-fmicb.2023.12-Growth-enhancing-effect-of-Actinocyclus-diatom-associated-bacteria

This repositorey contain the dada2 pipeline used to process the illumina sequence reads in the manuscript "Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp." (DOI: 10.3389/fmicb.2023.1230349)

Size: 73.2 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0