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Personal Cancer Genome Reporter (PCGR)

Tools to work with variant call format files

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Genotype_plot ⭐ 68

A set of functions to visualise genotypes based on a VCF

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

Cancer Predisposition Sequencing Reporter (CPSR)

Analysis_pipeline ⭐ 40

TOPMed analysis pipeline

Gwasglue ⭐ 28

Linking GWAS data to analytical tools in R

Cnv_facets ⭐ 26

Somatic copy variant caller (CNV) for next generation sequencing

Gwaspipeline ⭐ 26

An R package for predicting HR deficiency from mutation contexts

1000_genomes_examples ⭐ 23

Examples using R and 1000 genomes data

Proxysnps ⭐ 21

🔖 Get SNP proxies from the 1000 Genomes Project.

Nf Gwas Pipeline ⭐ 17

A Nextflow Genome-Wide Association Study (GWAS) Pipeline

Sigprofilermatrixgeneratorr ⭐ 17

R wrapper for utilizing the SigProfilerMatrixGenerator framework

Hrdetect Pipeline ⭐ 15

Neoantimon ⭐ 12

A manuscript is at bioarxiv.

Psap Pipeline ⭐ 12

Sigprofilerextractorr ⭐ 11

An R wrapper for SigProfilerExtractor that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Interactive table from gemini output

Maf Summary ⭐ 10

Summary of a single or multiple MAF files.

Splicing Prediction Pipeline

Gbs_snp_filter ⭐ 10

filtering SNPs based on LD and HWE status

Preinvasive ⭐ 9

Molecular analysis of pre-invasive lung cancer samples

Gwas Vcf Specification ⭐ 9

Specification for the GWAS-VCF format (manuscript in preparation)

R functions for generating site frequency spectra (SFS) from a VCF file.

Scnaphase ⭐ 8

Profile haploid somatic copy number alterations,especially for NGS sequencing data on significantly contaminated tumor samples

R Bindings for htslib/bcf

Simulation of rare and common variants based on 1000 genomes data

Optimizing Cancer Mutation Signatures Jointly with Sampling Likelihood

Cegwas2 Nf ⭐ 7

GWA mapping with C. elegans

Tumor-only variant calling

Michigan Imputation Helper ⭐ 6

Hmzdelfinder ⭐ 6

CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data

Tao Yan's Plot Toolkit

A collection of scripts I wrote when doing population genetics: calculate GC content, perform the McDonald-Kreitman test, calculate Tajima's D, convert VCF files to FASTA files using a reference genome

Vcfwrenchr ⭐ 5

Basic R package for VCF reformatting (json and tab-delimited text)

Significantly Mutated Region Finder

These scripts reformat a VCF into a SQLite database, with R

Scripts for the optimization of RADseq clustering thresholds in population genetics

Neoepprocessing ⭐ 5

Collection of scripts for pre- and postprocessing neoantigen discovery calls.

Biscuiteer ⭐ 5

tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output

Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer

visual analysis of your VCF files

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