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CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data

Python 15 Updated Jan 20, 2025
Python 9 4 Updated Jan 22, 2025

Blazing fast inference of PLN models built on top of Python and PyTorch

Python 7 1 Updated Jan 23, 2025

Toolkit for processing sequences in FASTA/Q formats

C 1,414 307 Updated Aug 10, 2024

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

R 150 25 Updated Mar 22, 2023

Variable Selection Using Random Forests

R 36 10 Updated Jul 11, 2024

Network construction, analysis, and comparison for microbial compositional data

R 159 28 Updated Dec 10, 2024

Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis

Python 12 10 Updated Jan 14, 2025

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Perl 484 150 Updated Dec 18, 2024

🍄 Qiime2 ITS classifiers for the UNITE database

HTML 36 5 Updated Jul 13, 2024

A GlobalProtect VPN client for Linux, written in Rust, based on OpenConnect and Tauri, supports SSO with MFA, Yubikey, and client certificate authentication, etc.

Rust 1,468 163 Updated Jan 22, 2025

Line-by-line profiling for Python

Python 2,819 123 Updated Jan 18, 2025

A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment.

Python 643 112 Updated Jul 29, 2024

Repository containing lists of all published ancient metagenomic (and related) samples and libraries

HTML 68 33 Updated Jan 14, 2025

A curated list of awesome ggplot2 tutorials, packages etc.

1,611 169 Updated Jan 19, 2025

Combination matrix axis for 'ggplot2' to create 'UpSet' plots

R 354 26 Updated Jun 24, 2024

This repo collects the list of learning online resources related to microbiome computational science and tools.

80 12 Updated Nov 14, 2024

🚥 Visualizing publication-quality multiple sequence alignment using ggplot2

R 207 23 Updated Dec 20, 2024

A Rich renderable for viewing Multiple Sequence Alignments in the terminal.

Python 78 2 Updated May 31, 2022

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Python 132 33 Updated Dec 20, 2024

Build a partitioned pangenome graph from microbial genomes

Python 250 31 Updated Jan 9, 2025

A grammar of graphics for comparative genomics

R 636 65 Updated Dec 5, 2024

Bioinformatics tool to find integrons in bacterial genomes

F* 68 22 Updated Jun 6, 2024

IS mapping software

Python 53 16 Updated Dec 3, 2021

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

Python 88 16 Updated Nov 16, 2023

Curation of Antibiotic Resistance Genes by using crowdsourcing

CSS 9 2 Updated Jan 12, 2023

Fast Whole-Genome Similarity (ANI) Estimation

C++ 385 67 Updated Jan 10, 2024

This repo collects the list of conferences/meetings/workshops etc. related to microbiome science and tools.

48 5 Updated Jan 14, 2025

Open source code for AlphaFold 2.

Python 13,109 2,317 Updated Dec 20, 2024

EGGO database and code for associated manuscript

R 7 1 Updated Feb 3, 2022
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