miachom Goto Github PK

blog

canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.

comut_plots

crpc-sv-pattern-study

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

gatk_mutect2

genomeinfodb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

gistic2

Genomic Identification of Significant Targets in Cancer (GISTIC), version 2

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

machom.github.io

mutect2_snakemake

phylogicndt

Forked repository of the PhylogicNDT code with updates to get the dockerfile working

purecn

Copy number calling and variant classification using targeted short read sequencing

rna-seq-vn-lab

sequence-manipulation

snakemake-trcc

Personal repository to store syntax, examples and notes for Snakemake collected from different resources

sv_10x_analysis

Structural variation analysis of 10X Genomics linked-read data

synteny_match

terra-gs-utilities

titancna_10x_snakemake

Snakemake workflow for 10X Genomics WGS analysis using TitanCNA - GavinHaLab Forked Repo. Fixed the Issue I was getting from the original repo: Error: RangedData objects are deprecated and the coercion method from data.frame or DataTable to RangedData is now defunct. Please migrate your code to use GRanges or GRangesList objects instead.

topgo

useful-bash