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aldy

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

arriba

Fast and accurate gene fusion detection from RNA-Seq data

asneo

circular-binary-segmentation

cnvnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

complex-upset

A library for creating complex UpSet plots with ggplot2 geoms

data-science-at-the-command-line

Data Science at the Command Line

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

dnafeaturesviewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

dualmarker

R package for data visulization and exploration of dual biomarkers

elabftw

:notebook: eLabFTW is the most popular open source electronic lab notebook for research labs.

enhancedvolcano

Publication-ready volcano plots with enhanced colouring and labeling

fastq-screen

Detecting contamination in NGS data and multi-species analysis

fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

fusioninspector

FusionInspector code

genefuse

Gene fusion detection and visualization

ggheatmap

ggplot2 version of heatmap

haplotypetools

A toolkit for identifying recombination and recombinant genotypes

hla-la

Fast HLA type inference from whole-genome data

hotnewsanalysis

利用文本挖掘技术进行新闻热点关注问题分析

intervar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline

kraken2

The second version of the Kraken taxonomic sequence classification system

leetcode

Python & JAVA Solutions for Leetcode

metasv

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing

mrlocus

Mendelian Randomization of gene expression (exposure) on GWAS traits (outcome). See website for software usage guide:

neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery

neofusion

neopredpipe

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.

optitype

Precision HLA typing from next-generation sequencing data

panclassif

A method to improve TCGA pancancer classifiers performance