welch16
I am a computational biologist at the Ong lab in UW-Madison's BMI department. I am interested in data integration, and reproducible research.
University of Wisconsin, MadisonMadison, Wisconsin
Pinned Repositories
ChIPexoQual
A quality control pipeline for ChIP-exo/nexus samples.
ChIPUtils
A package with basic utilities for ChIP analysis (both ChIP-seq and ChIP-exo)
cisr2021singlecellRNA
UWCCC 2021 single cell RNA-seq tutorial
gwas_vitamind_african_ancestry
Code for the "Genome-wide association study (GWAS) and functional analysis of genetic variants associated with circulating vitamin D binding protein in African Americans
profile_slides
rwlib
Functions that I use often
Segvis
Package to visualize next generation sequencing data along genomic regions
welch16's Repositories
welch16/gwas_vitamind_african_ancestry
Code for the "Genome-wide association study (GWAS) and functional analysis of genetic variants associated with circulating vitamin D binding protein in African Americans
welch16/ChIPexoQual
A quality control pipeline for ChIP-exo/nexus samples.
welch16/ChIPUtils
A package with basic utilities for ChIP analysis (both ChIP-seq and ChIP-exo)
welch16/cisr2021singlecellRNA
UWCCC 2021 single cell RNA-seq tutorial
welch16/rwlib
Functions that I use often
welch16/Segvis
Package to visualize next generation sequencing data along genomic regions
welch16/microbiome.onglab
A wrapper for dada2
welch16/BISCUIT_SingleCell_IMM_ICML_2016
R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.
welch16/ChIPexo
ChIP-Exo is a new techonology for sequencing which obtains a higher accuracy to predict TFBS
welch16/ChIPexoQualExample
Example data for the ChIPexoQual pacakge
welch16/complex-upset
A library for creating complex UpSet plots with ggplot2 geoms
welch16/create_bioc_package
Slides about my experience creating a bioconductor package
welch16/drake_slides
slides for group meeting about using drake
welch16/EBV_NOK
Repository for a study of the biological effects of EBV in epithelial cells
welch16/fastqcr
fastqcr: Quality Control of Sequencing Data
welch16/FMHighLD
welch16/ggtech
ggplot2 tech themes, scales, and geoms
welch16/ihw_slides
Group meeting presentation about IHW
welch16/intro_to_llm
welch16/microbiome-pipeline
A pipeline for processing 16S / ITS data
welch16/ML-X-Nexus
welch16/mmmisc
My Library of R Helpers
welch16/recursive_elimination_by_sensitivity_testing
This repo provides a novel feature selection algorithm called Recursive Feature Elimination by Sensitivity Testing.
welch16/renewelch.me
welch16/snakemake-demos
Example Snakefiles for various use cases
welch16/tcr
tcR: an R package for immune receptor repertoire advanced data analysis.
welch16/UWCCC.GWAS
welch16/vegan
R package for community ecologists: popular ordination methods, ecological null models & diversity analysis
welch16/xaringan
Presentation Ninja 幻灯忍者 · 写轮眼
welch16/YY1_chipseq_tracks