Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

ClassifyCNV: a tool for clinical annotation of copy-number variants

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.

Bioinformatics CNV Detection with Random Forest Model

Hidden Markov Model based Copy number caller

A new CNV calling method for DNA-seq data

TCGA hg19 and hg38 data downloader.

Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files

An adaptable method for analyzing SNVs, INDELs, and CNVs from Whole Exome Sequencing (WES) data, emphasizing germline variants.

In this repository I backup the pipelines I write for the project I am involved

The performance of individual CNV detection software and state-of-the-art sequencing. All analyses were performed using the Python and R programming languages.

A high-accuracy tool for integrating scDNA-seq and scRNA-seq data

CNV DB Adapter

Within-sample CNV calling

Visualization of CNV distribution organized in genomic ordering, using scRNAseq data.

AnnotSV project to work with MongoDB and FastAPI, made for cnvhub.net

A simple module for diagnostic variant information parsing

A Snakemake pipeline for copy number variant calling without normal tissue samples

A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).