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differential-abundance-analysis

Here are 15 public repositories matching this topic...

yiluheihei / microbiomeMarker

R package for microbiome biomarker discovery

r metagenomics microbiome r-package biomarker-discovery lefse differential-abundance-analysis

Updated Nov 4, 2023
R

biobakery / Maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

tools public metagenomics bioconductor repeated-measures microbiome false-discovery-rate biobakery differential-abundance-analysis multiple-covariates

Updated Nov 11, 2024
R

FrederickHuangLin / ANCOMBC

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

correlation sequencing microbiome normalization secom differential-abundance-analysis ancom ancombc ancombc2

Updated Oct 21, 2024
R

FrederickHuangLin / ANCOM-BC-Code-Archive

Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check our ANCOMBC R package for the most up-to-date ANCOM-BC function.

sequencing microbiome normalization differential-abundance-analysis ancom ancom-bc

Updated Oct 19, 2020
HTML

himelmallick / Tweedieverse

Differential analysis of multi-omics data based on the Tweedie distribution

metagenomics microbiome single-cell differential-expression multi-omics-data differential-abundance-analysis

Updated Aug 8, 2024
R

mikemc / differential-abundance-theory

A manuscript exploring the effects of taxonomic bias on microbiome differential-abundance analysis.

measurements manuscript bias differential-abundance-analysis absolute-abundances

Updated Oct 30, 2023
HTML

FrederickHuangLin / Microbiome-Review-Code-Archive

Data, scripts, and outputs for the npj Biofilms and Microbiomes paper "Analysis of microbial compositions: A review of normalization and differential abundance analysis"

microbiome differential-abundance-analysis

Updated Aug 23, 2020
HTML

himelmallick / BenchmarkMicrobiome

Large-scale Benchmarking of Microbial Multivariable Association Methods

benchmarking metagenomics repeated-measures microbiome false-discovery-rate differential-abundance-methods synthetic-dataset-generation biobakery differential-abundance-analysis multiple-covariates

Updated Feb 2, 2021
R

shuangj00 / BMDA

A Bayesian model for the differential abundance analysis of microbiome sequencing data

microbiome-data zinb-dpp differential-abundance-analysis

Updated May 31, 2024
R

biobakery / maaslin2_benchmark

Large-scale Benchmarking of Microbial Multivariable Association Methods

benchmarking public metagenomics repeated-measures microbiome benchmark-framework false-discovery-rate differential-abundance-analysis multiple-covariates

Updated Nov 14, 2020
R

himelmallick / TweedieLabs

Collection of walkthrough tutorials on how to use Tweedieverse for differential analysis of omics data.

metagenomics scrna-seq microbiome differential-expression differential-analysis multi-omics differential-abundance-analysis

Updated Feb 26, 2022
HTML

iliapopov17 / The-shadow-of-HIV

🦠Research project in Bioinformatics Institute 2023-2024

snakemake dna beta-diversity iontorrent hiv samtools bowtie2 relative-abundances alpha-diversity kraken2 differential-abundance-analysis maaslin2

Updated Aug 16, 2024
Jupyter Notebook

TaschnerMandlGroup / MapMetSC

MAPping METastases in Neuroblastoma - spatially and temporally

quality-control correlation-analysis differential-abundance-analysis cell-clustering

Updated Oct 8, 2024
R

MicrobialGenomics-IrsicaixaOrg / dar

dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.

feature-selection rstats bioconductor microbiology microbiome biomarker-discovery phyloseq differential-abundance-analysis

Updated Oct 16, 2024
R

NIGMS / Proteome-Quantification

Secondary analysis of Proteomics data in R, developed by the University of Arkansas for Medical Sciences for the NIH NIGMS Sandbox project.

aws bioinformatics jupyter-notebook gcp data-visualization cloud-computing proteomics mass-spectrometry data-preprocessing r-programming differential-abundance-analysis nih-nigms-sandbox

Updated Nov 21, 2024
Jupyter Notebook

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