iliapopov17/NGS-Data-Analysis-Manual

Repository for manuals for NGS data analysis

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cafferychen777/MicrobiomeStat

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

Language: R - Size: 15.7 MB - Last synced: about 15 hours ago - Pushed: 1 day ago - Stars: 24 - Forks: 3

LAACit/Tesis_Metataxonomica_manglar_yucat-n_16sRNA

Tesis licenciatura "Metataxonómica de bacterias comoindicador de la descarga de xenobióticos por el Anillo de Cenotes en el sedimento de manglar rojo"

Language: R - Size: 21.5 KB - Last synced: about 19 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

jinhuili-lab/MicrobioSee2

MicrobioSee2, a desktop sofware for visulization of microbiome result, which contian multiple modules, such as Alpha Diversity, Beta Diversity, Species Conpositions, volcano plot, and pie chart.

Language: HTML - Size: 567 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

ravel-lab/speciateIT

Fast, accurate taxonomic assignments for the human vaginal microbiota

Language: HTML - Size: 138 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 6 - Forks: 4

grimmlab/MicrobiomeBestPracticeReview

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

Language: Shell - Size: 13 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 101 - Forks: 36

TessaBeaver/TBeaver-G-childressi-microbiome-analysis

Microbial community dynamics during key life-history transitions in the chemosymbiotic mussel, Gigantidas childressi

Language: R - Size: 17.6 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

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: 7 days ago - Pushed: 7 days ago - Stars: 2 - Forks: 2

IMCBioinformatics/dada2_snakemake_workflow

Amplicon sequencing workflow with snakemake and dada2

Language: R - Size: 972 KB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 2 - Forks: 1

SchlossLab/mothur-snakemake-workflow

Snakemake template for microbial amplicon sequence analysis with mothur.

Language: Python - Size: 949 KB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 3 - Forks: 0

xapple/crest4

The `crest4` python package can automatically assign taxonomic names to DNA sequences obtained from environmental sequencing.

Language: Python - Size: 1.16 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 5 - Forks: 0

cafferychen777/ggpicrust2

Make Picrust2 Output Analysis and Visualization Easier

Language: R - Size: 21.2 MB - Last synced: 15 days ago - Pushed: about 2 months ago - Stars: 83 - Forks: 10

Shuyib/Phylogenetic-tree-study

Estimating Phylogenetic trees using six microorganisms 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7

Language: Jupyter Notebook - Size: 3.45 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 3 - Forks: 5

BCCDC-PHL/16s-nf

Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.

Language: Python - Size: 51.8 KB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 2 - Forks: 0

tmbuza/iMAP

iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline

Language: HTML - Size: 160 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 14 - Forks: 4

jedick/chem16S

Chemical metrics for microbial communities

Language: R - Size: 8.6 MB - Last synced: 11 days ago - Pushed: about 1 month ago - Stars: 4 - Forks: 0

Shuyib/mouse_gut_OTU

Vectorization and Unsupervised Learning of Mouse Operation Taxonomic Units to determine which species of bacteria form distinct groups in a dataset.

Language: Jupyter Notebook - Size: 91.8 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 1

segrelab/MiCoNE-pipeline-paper

The source code for the MIND pipeline paper

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hsmurali/Transitive_Annotation

The impact of transitive annotation on the training of taxonomic classifiers

Language: Jupyter Notebook - Size: 2.43 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

nlabrad/CIMS-Cyanobacterial-ITS-motif-slicer

A tool to identify and extract the commonly used ITS folding motifs from a 16s-23s rRNA sequence.

Language: Python - Size: 6.06 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

segrelab/MiCoNE

The Microbial Co-occurrence Network Explorer

Language: Python - Size: 75.1 MB - Last synced: 22 days ago - Pushed: 7 months ago - Stars: 18 - Forks: 4

Ebedthan/hyperex

Hypervariable region primer-based extractor for 16S rRNA and other SSU/LSU sequences.

Language: Rust - Size: 403 KB - Last synced: 13 days ago - Pushed: about 1 month ago - Stars: 9 - Forks: 1

LMG9509/TFM

Evaluación del impacto del proceso de rarefacción en la detección de comunidades microbianas en datos de amplicones ARNr 16S

Language: R - Size: 83 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

microsud/Tools-Microbiome-Analysis

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

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raymondkiu/16S_extraction_Barrnap

Automated 16S sequence extraction using Barrnap output gff files

Language: Shell - Size: 3.91 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 1

raymondkiu/bactspeciesID

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

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genid/TissueID

A novel taxonomy-independent deep learning microbiome approach allow for accuaret classification of human epithelial materials

Language: Python - Size: 8.25 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

tianrenmao/16S-18S-ITS-ASAP

This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequences.

Language: Perl - Size: 23.8 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 0

oschakoory/RiboTaxa

RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

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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

sielerjm/ZF-Diet_Infection

Code used for analysis in the publication: Disentangling the link between zebrafish diet, gut microbiome succession, and Mycobacterium chelonae infection.

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segalmicrobiomelab/lung_cancer_microbiome

Language: R - Size: 27.3 KB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 7 - Forks: 2

dschnei1/ngs4ecoprod

NGS4ECOPROD - An easy-to-use conda environment and pipelines for metagenome sequence analysis

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rjstevick/loperamide-zebrafish-dysbiosis

Analysis of 16S rRNA and in vitro data from larval zebrafish with loperamide treatment

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rjstevick/PJnitrogenOysterMicrobiomes

Study of farmed oysters and nitrogen cycling in Point Judith Pond, RI. Scripts for analysis of 16S rRNA amplicon and metatranscriptomic data.

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leahkemp/running_16S_rRNA_pipeline

Trying to help a colleague get a 16s-rRNA-Sanger snakemake pipeline working.

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rjstevick/NBayTNCoystersAnalysis

Scripts for analysis of metatranscriptomic and 16S rRNA amplicon data from wild oysters in Narragansett Bay

Language: R - Size: 21.8 MB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 1

ali-kishk/AmpliconNet

Sequence based 16S rRNA Taxonomic classifier using MLP

Language: Jupyter Notebook - Size: 296 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 8 - Forks: 0

hsmurali/SCRAPT

SCRAPT: An Iterative Algorithm for Clustering Large 16S rRNA Gene Datasets

Language: Jupyter Notebook - Size: 13.9 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

xapple/pacmill

The `pacmill` python package is a bioinformatics pipeline that is developed to process microbial 16S amplicon sequencing data and produce PDF reports detailing taxonomical assignments along with other statistics.

Language: Python - Size: 14.9 MB - Last synced: 21 days ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

rwst/process-ubiome-16S 📦

process raw reads from ubiome

Language: Python - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 0

rjstevick/zebrafish-conv-mix9-models

Analysis of 16S rRNA and microscopy data from larval zebrafish

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dizak/mothulity

Easy-to-use tool facilitating work with Mothur.

Language: JavaScript - Size: 29.3 MB - Last synced: 24 days ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 3

Nucleomics-VIB/16S_analysis_pipeline

Building a pipeline for automated 16S analysis from paired short-reads or long-reads

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achillesrasquinha/16SMaRT

16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).

Language: Python - Size: 2.77 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 7 - Forks: 0

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

JordyCoolen/RC-PCR_CLASSIFIER

Reverse Complement PCR (RC-PCR_ Classification pipeline.

Language: Python - Size: 1.44 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

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

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

astrdhr/metagenomics-soil

BSc project: metagenomic analysis of urban park soil. Breakdown of some of the code I used can be viewed on this website:

Language: Shell - Size: 37 MB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

mmtechslv/PhyloMAF

Next Generation Phylogenetic Microbiome Analysis Framework

Language: Python - Size: 86.5 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

Kur1sutaru/16SrDNA_stats Fork of tiagofalconlopes/16SrDNA_stats

A simple code to analyze OTU table and RNA-seq normalization in R

Language: R - Size: 14.7 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

apredeus/yakutica

Analysis scripts for Gortzia yakutica paper

Language: R - Size: 697 KB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 1 - 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

rjstevick/AllNBayWildOystersCombined

Scripts for combined 16S analysis and Rscripts to make figures for conclusions chapter of dissertation

Language: R - Size: 4.73 MB - Last synced: 11 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

rjstevick/RWUOysterHatcheryProbiotics16S

Scripts for analysis of 16S data from the RWU Oyster Hatchery Probiotic trials

Size: 1.01 MB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

cometsong/mbiome_seqrun_qc

List of sequencer runs; QC and run Info from each run, modular display of all existing (uploaded) types of info and statistics.

Language: Python - Size: 2.97 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

mruehlemann/phaat

PAAT uses phylogenetic trees to refine differential abundance signals

Language: R - Size: 1.36 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

accoleon/pipping

Code and report for a small tool to optimize 16S sequencing pipelines

Language: C - Size: 24.7 MB - Last synced: about 1 month ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0

glickmac/Microbiome_Demo

A repository containing a demo microbiome workflow for R and Python

Language: Jupyter Notebook - Size: 127 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

gaarangoa/chfilter

Chloroplast 16S removal from Metagenomics samples (or any NGS samples)

Language: Python - Size: 8.22 MB - Last synced: 12 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0