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accucopy

Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.

adap-in-mzmine2

allele_freq_map

R script for visualising allele frequency on world map

allelefrequencies

📂 HLA allele frequencies in tab-delimited format, downloaded from AFND.

app-gc

Data preprocessing pipeline for GC- and GCxGC-MS raw data

assign-taxonomy-with-blast

Assign taxonomy with blast, can be used for qiime

aws-gatk-recipe-nextflow-pipeline

barmen_exome_capture

BenchmARking from Mobidic for Exome sequencing at Nucleotide scale

blacklist

Application for making ENCODE Blacklists

circle-map

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

circle_finder

Micro DNA identification

circos

R script to make Circos figure

cloudgene

A framework to build Software As A Service (SaaS) platforms for data analysis pipelines.

cmuteam_nf_pipeline

CMUTEAM pipeline based on Nextflow and Docker container

compvar-workshop-docs

Documentation for the 2018 Genome Analysis workshop I gave in Helsinki

covid19_imaging_ai_paper_list

COVID-19 imaging-based AI paper collection

cyclomics_consensus_pipeline

Cyclomics consensus pipeline based on LAST and dagcon

deep-hla

Upload test

deepgoplus

DeepGO with GOPlus axioms

delfi_scripts

docker

Source Dockerfiles for images: https://hub.docker.com/u/shengwei

exome_capture

faces-mtl

Multi Task Learning example with Keras

genome_tools

tools for genome

getgn

Script for getting gene neighborhoods in specified region

glassgo_postprocessing

graphprot

GraphProt: modelling binding preferences of RNA-binding proteins

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

gut_microbiota_workshop_cmuteam_2022

gwas-lecture

Lectures on Genome Wide Association Studies (GWAS) using Python, Limix and Jupyter Noteboos