A fast tool for detecting and decomposing segmental duplications in genome assemblies

Neural network classification of TE

Scripts and pipelines used in the preprint Bortoluzzi et al. (2024)

Summary fastq reads, bases, Q20, Q30, N bases, GC

R package to print maps, draw on them, and scan them back in

Making phylogenies for a list of fish species

Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with…

A shiny application to visualize MCscan result

Quantify ancestral linkage group rearrangement in chromosome-level genomes

Polygenetic Basis of Seedlessness in Grapevine (Vitis vinifera L.)

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

Data, Code, and Visualizations for the #30DayMapChallenge

Color palette package in R inspired by works at the Metropolitan Museum of Art in New York

Phyloclimatic modeling: estimation of ancestral climatic niches, age-range-correlation, niche equivalency test and background-similarity test.

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.

Modular framework for deep learning predictions on methylation data.

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

A snakemake workflow for de novo genome assembly. It produces chromosome-scale primary/phased assemblies complete with organelles (mitochondrion and/or chloroplast). It automatically assesses the q…

单细胞分析的中文pipeline

bisulfite sequencing pipeline from fastq to methylation reports

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline

R package for genomic feature analysis and visualization

List of software packages for multi-omics analysis

Genome browser and variant annotation

Code used during studying the chromosomal rearrangements in Ae. umbellulata