lumpy: a general probabilistic framework for structural variant discovery

Integrative Structural Variant analysis

Python tool for converting files and office documents to Markdown.

Nature Methods: RNA foundation model (together with RhoFold)

Code of a structure-enhanced RNA language model named ERNIE-RNA

A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.

A TUI for monitoring Snakemake workflows in real-time.

Real time monitor for snakemake

Monitor computational workflows in real time

Feature-rich Python implementation of the tximport package for gene count estimation.

The fully R based tool peakCombiner is a user-friendly, transparent, modular and customizable package with the purpose to create a consensus peak file from genomic input regions. The aim is to allo…

Yet another redundant workflow engine

Open-source bioinformatics components for Dash

Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired-end reads in fastq files from amplicon sequencing

An interactive explorer for single-cell transcriptomics data

Variance decomposition using conditional variational auto-encoders

ShellCheck, a static analysis tool for shell scripts

Gene Fusion Visualiser

Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.

fast webservices based query tool for large sets of genomic features

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.

The Zavolab Automated RNA-seq Pipeline

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

Mulled - Automatized Containerized Software Repository

Multi-origin batch effect remover method

scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics