RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Comprehensive genome annotation pipeline for plant combining EVM/PASA, GETA, AUGUSTUS and Helixer with semi-supervised filtering for high-quality gene models.

BRAKER re-implemented with snakemake

An integrative pipeline for family-level super-pangenome analysis across coding and noncoding sequences.

longcallR is a tool for SNP calling, haplotype phasing, and allele-specific analysis with long-read RNA-seq data.

The uncompromising Snakemake code formatter

Command-line toolkit for Gene Ontology (GO) enrichment analysis

Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome

2+ genomes make a parTEA! This pangenome TE annotation pipeline extends EarlGrey for multi-genome comparative analysis

Genome modeling and design across all domains of life

Co-expression & functional inference of biosynthetic gene clusters

MACS -- Model-based Analysis of ChIP-Seq

Infer a tree sequence from genetic variation data.

Population-scale Ancestral Recombination Graph (ARG) library

TF MOtif Discovery from Importance SCOres

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Vim notebook cell bindings for JupyterLab

Creating alignment plots from bam files

The ERGA Assembly Reports repository 👂

Comparative pan-metagenomic graph.

Fast Species Tree Inference

No-as-a-Service (NaaS) is a simple API that returns a random rejection reason. Use it when you need a realistic excuse, a fun “no,” or want to simulate being turned down in style.

DANSE: Dynamics inference Algorithm on Networks Specified by Enhancers

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.

A software suite for accurate identification, annotation, translation, and feature characterization of annotate transcripts.

long read RNA-seq quantification