List of software packages for multi-omics analysis

A pipeline for analyzing bacterial genomic sequences. Easily.

This is the standalone version of the EviAnn pipeline

Understanding Deep Learning - Simon J.D. Prince

Pairwise whole genome aligner

Grammar of Scalable Linked Interactive Nucleotide Graphics

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

The EasyMultiProfiler package aims to offer a user-friendly and efficient multi-omics data analysis tool on the R platform. It facilitates various essential tasks related to microbiome, genome, and…

Batch Correction and Adaptive Contrast Calling in Complex RNA-seq Experimental Designs Using DESeq2

A high-throughput genotyping-by-sequencing (GBS) pipeline integrating DeepVariant and GLnexus for accurate variant calling in plant genomics.

A collection of scripts and notes related to genomics and bioinformatics

Developmental private RNASeq pipeline for bacterial quantification.

Miscellaneous bioinformatic helper scripts for various tasks

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two rapidly evolving accessory chromosomes

CLI tool to process and analyze MAF files ( Multiple alignment format )

ggplot2: elegant graphics for data analysis

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

Telomere-to-telomere of ChineseQuartet (CQ)

A tool for generating consensus long-read assemblies for bacterial genomes

Bioinformatics tool for Locus Visualisation

simple tools for data cleaning in R

Repository for microbiome project investigating Enterobacteriaceae landscape across the world

Enhancement of Gut Microbial Diversity and Functional Profiling

Jupyter notebooks and other resources for Think Python by Allen Downey, published by O'Reilly Media.

order a FASTA file by microchromosome specific genes

well-documented demonstration Python Jupyter workflows for many common machine learning workflows

Genome Assembly 102