DNA sequencing analysis notes from Ming Tang
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Updated
Mar 26, 2023 - Shell
DNA sequencing analysis notes from Ming Tang
Microassembly based somatic variant caller for NGS data
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Multi-sample somatic variant caller
Clone identification from single-cell data
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
ClairS - a deep-learning method for long-read somatic small variant calling
Galaxy Tool Shed repositories maintained and developed by the Morin Lab.
Transposon Insertion Finder - Detection of new TE insertions in NGS data
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
knowledge-based genotyping of cancer hotspots from the tumor BAM files
📦 An R package for inferring the mutational exposures difference between groups.
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
Snakemake workflow for somatic mutation detection without matched normal samples
Polymorphic Edge Detection - An efficient polymorphism detector for NGS data
Tumor-only variant calling
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