Easy Copy Number !

• UpdatedOct 18, 2021
• R

Pipeline for Somatic Variant Calling with WES and WGS data

• UpdatedMay 7, 2024
• Python

Please consider using/contributing tohttps://github.com/nf-core/sarek

• UpdatedJan 3, 2019
• Nextflow

Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data

• UpdatedMar 18, 2023
• R

A fork of the project Excavator2 from sourceforge.

• UpdatedJun 29, 2017
• R

This pipeline has moved! Please see:

• UpdatedApr 18, 2018
• Groovy

Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

• UpdatedOct 22, 2024
• R

• UpdatedOct 2, 2017
• Perl

Scripts used on a cluster that demonstrate vcf file manipulation and preparation.

• UpdatedMar 9, 2020
• Shell

The transplot package can be used to make multi-track plots of Next Generation Sequencing (NGS) data for gene transcripts, namely for depth of coverage and for the distribution of variants and protein domains.

• UpdatedMay 31, 2018
• Python

As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of …

• UpdatedDec 11, 2019
• R

Main Repository for my MASTER'S THESIS PROJECT

• UpdatedDec 13, 2022
• Python

Selects possible pathogenic variants from an Alamut output

• UpdatedJun 12, 2018
• Ruby

colorectal cancer

• UpdatedJun 15, 2018

Scripts and data processing notes for Russian exome sequencing AF paper

• UpdatedJul 24, 2020
• R

Miscellaneous pipelines for genomics computation analysis in a SGE HPC platform.

• UpdatedJan 15, 2020
• Shell

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

• UpdatedNov 26, 2024
• R

Note: This is a detailed Intro to this project. A brief users guide can be found at users_guide.md

• UpdatedAug 19, 2019
• Jupyter Notebook

Leveraging WES short reads for PAN-EXOME creation and analysis.

• UpdatedNov 6, 2024
• WDL

COverage Analysis Tool have been developed in 2016. It aims to automatically find bad quality regions of coding sequences in a set of sequencing data. It includes a graphical interface.

• UpdatedJul 23, 2019
• Python