116 Open source projects that are alternatives of or similar to DAtest

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

Metagenomics calibration R package

R package for microbiome biomarker discovery

MaAsLin2: Microbiome Multivariate Association with Linear Models

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

pyQms, generalized, fast and accurate mass spectrometry data quantification

Various functions for analysis of microbial community data

Collection of commonly used RDP Tools for easy building

Quantitative features for mass spectrometry data

🚀 A sequencing simulator

Predict AMPs in (meta)genomes and peptides

The repo for LFQ-Analyst

Deep learning for Metagenome Assembly Error Detection

Open source Java library for computational proteomics

AMBER: Assessment of Metagenome BinnERs

A robust, extensible metagenomics pipeline

RHermes is a semi-targeted metabolomics package to deeply characterize biological and environmental samples.

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

Interpretation of proteomics identification results

Import and summarize transcript-level estimates for gene-level analysis

Rapid Calculation of Model Metrics

Improving genome bins through the combination of different binning programs

A proof of concept of RNAseq pipeline

Meta-Omics Software for Community Analysis

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

Porting DESeq2 and DEXSeq into python via rpy2

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

📚 🔬 PIA - Protein Inference Algorithms

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Discrete Distributional Differential Expression

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

Feature Annotation Location Description Ontology

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

gargammel is an ancient DNA simulator

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

Galaxy tools for metabolomics maintained by Workflow4Metabolomics

Interactive visualizations for differential expression

A Comet-based, best practices proteomics pipeline.

Differential expression analysis for single-cell RNA-seq data.

Visualize microbiome data with black magic ggtree

Public Workflows at GNPS

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Documentation for GNPS and related tools as written in mkdocs

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

No description or website provided.

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

A proof of concept RNA-Seq pipeline with Nextflow

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

This repo contains regression and classification projects. Examples: development of predictive models for comments on social media websites; building classifiers to predict outcomes in sports competitions; churn analysis; prediction of clicks on online ads; analysis of the opioids crisis and an analysis of retail store expansion strategies using…

Modeling and correcting fragment sequence bias for RNA-seq

Exome/Capture/RNASeq Pipeline Implementation using snakemake

The MG-RAST Backend -- the API server

Cross-disease comparison of case-control gut microbiome studies

Analysing Capture Seq Count Data

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Fast and flexible semi-supervised learning for peptide detection in Python

Prize-Collecting Steiner Forests for Interactomes