Topic: microbiome Goto Github
Some thing interesting about microbiome
Some thing interesting about microbiome
microbiome,Accurate sample inference from amplicon data with single nucleotide resolution
User: benjjneb
Home Page: http://benjjneb.github.io/dada2/
microbiome,Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
User: benjjneb
Home Page: https://benjjneb.github.io/decontam/
microbiome,MaAsLin2: Microbiome Multivariate Association with Linear Models
Organization: biobakery
Home Page: http://huttenhower.sph.harvard.edu/maaslin2
microbiome,Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Organization: biobakery
Home Page: http://huttenhower.sph.harvard.edu/melonnpan
microbiome,Emperor a tool for the analysis and visualization of large microbial ecology datasets
Organization: biocore
Home Page: http://biocore.github.io/emperor/
microbiome,A fast and scalable phylogenetic tree viewer for microbiome data analysis
Organization: biocore
microbiome,Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
Organization: biocore
microbiome,Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Organization: biocore
microbiome,Sample search by metadata and features
Organization: biocore
microbiome,Make Picrust2 Output Analysis and Visualization Easier
User: cafferychen777
Home Page: https://cafferychen777.github.io/ggpicrust2/
microbiome,Cross-disease comparison of case-control gut microbiome studies
User: cduvallet
microbiome,R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
User: david-barnett
Home Page: https://david-barnett.github.io/microViz/
microbiome,For analysis of microbiome and microbial community data
Organization: ecojulia
microbiome,: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
User: franciscozorrilla
Home Page: https://franciscozorrilla.github.io/metaGEM/
microbiome,Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM function.
User: frederickhuanglin
Home Page: https://www.tandfonline.com/doi/full/10.3402/mehd.v26.27663
microbiome,Differential abundance (DA) and correlation analyses for microbial absolute abundance data
User: frederickhuanglin
Home Page: https://www.nature.com/articles/s41467-020-17041-7
microbiome,PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:
Organization: genular
Home Page: https://genular.org
microbiome,The Microbiome Interpretable Temporal Rule Engine
Organization: gerberlab
microbiome,Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Organization: grimmlab
Home Page: https://www.bit.cs.tum.de/
microbiome,Visualize microbiome data with black magic ggtree
User: lch14forever
microbiome,Human Microbiome wiki
User: maximiliankohler
Home Page: https://HumanMicrobiome.info
microbiome,Inference of microbial interaction networks from large-scale heterogeneous abundance data
Organization: meringlab
microbiome,Python package to study microbial communities using metabolic modeling.
Organization: micom-dev
Home Page: https://micom-dev.github.io/micom
microbiome,DeepMicrobes: taxonomic classification for metagenomics with deep learning
User: microbelab
Home Page: https://doi.org/10.1093/nargab/lqaa009
microbiome,Microbiome analysis
Organization: microbiome
Home Page: https://microbiome.github.io/mia/
microbiome,microbiome R package
Organization: microbiome
microbiome,Orchestrating Microbiome Analysis
Organization: microbiome
Home Page: https://microbiome.github.io/OMA
microbiome,The is mostly a wrapper tool using phyloseq and microbiome R packages.
User: microsud
Home Page: https://microsud.github.io/microbiomeutilities/
microbiome,AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
User: nextgenusfs
Home Page: http://amptk.readthedocs.io/
microbiome,Amplicon sequencing analysis workflow using DADA2 and QIIME2
Organization: nf-core
Home Page: https://nf-co.re/ampliseq
microbiome,Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Organization: nf-core
Home Page: https://nf-co.re/taxprofiler
microbiome,ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
User: pirovc
Home Page: https://pirovc.github.io/ganon/
microbiome,Qiita - A multi-omics databasing effort
Organization: qiita-spots
Home Page: http://qiita.microbio.me
microbiome,Woltka: a versatile meta'omic data classifier
User: qiyunzhu
microbiome,Collection of commonly used RDP Tools for easy building
Organization: rdpstaff
microbiome,Compare different differential abundance and expression methods
User: russel88
microbiome,Various functions for analysis of microbial community data
User: russel88
microbiome,PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
Organization: segatalab
microbiome,Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
User: serka-m
microbiome,Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Organization: spaam-community
Home Page: http://www.spaam-community.org/AncientMetagenomeDir/
microbiome,Testing differences in cell type proportions from single-cell data.
User: stemangiola
Home Page: https://stemangiola.github.io/sccomp/
microbiome,A robust and fast clustering method for amplicon-based studies
User: torognes
microbiome,Versatile open-source tool for microbiome analysis
User: torognes
microbiome,Matrix dissimilarity from the differences of Moments and sparsity
User: tubanlee
Home Page: https://doi.org/10.5281/zenodo.10406288
microbiome,Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Organization: wrightonlabcsu
microbiome,16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
User: ycl6
microbiome,R package for microbiome biomarker discovery
User: yiluheihei
Home Page: https://yiluheihei.github.io/microbiomeMarker
microbiome,:microbe: A comprehensive R package for deep mining microbiome
Organization: yulab-smu
Home Page: https://www.sciencedirect.com/science/article/pii/S2666675823000164
microbiome,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.
User: zoecastillo
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