quinlan-lab

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

bedder-rs

an API for intersections of genomic data

sllobs-biostats

STRling

Detect novel (and reference) STR expansions from short-read data

vcf2db

create a gemini-compatible database from a VCF

ccrhtml

A small repo for storing the code for making the files and html for CCRs.

pathoscore

pathoscore evaluates variant pathogenicity tools and scores.

ccr

Building the constrained coding regions (CCR) model

bedqc

BED QC tool (in the making)

Snakemake_Tutorial

ceph-dnm-manuscript

Code used for figure generation and statistical analysis for https://elifesciences.org/articles/46922

human-rae-manuscript

code used for figure generation and statistical analysis for manuscript

STRling-nf

Nextflow implementation of STRling data flow

kmertools

covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

proj-mutator-mapping

Code for reproducing analysis and figures from https://elifesciences.org/reviewed-preprints/89096

transcriptionary

2022-10-11-Utah-Python

CEPH-K1463-TandemRepeats

covdist

simple coverage profile of aligned samples. useful for sequencing center feedback and topoffs.

exacresiduals

CCR model

facets-nf

nextflow implementation of the facets data flow.

freebayes-nf

a better freebayes-parallel

idplot

compare sequences to a shared root reference sequence.

mutator-epistasis-manuscript

preon

Precision Oncology data workflow

regionanalysis

Regional analysis folder

smoove-nf

Nextflow implementation of the smoove workflow and other tools for SV calling and QC

tmp

A temporary repository to transfer issues

uu-delphi-datascience