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2022-10-11-utah-python

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

bedder-rs

an API for intersections of genomic data

bedqc

BED QC tool (in the making)

ccr

Building the constrained coding regions (CCR) model

ccrhtml

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

ceph-dnm-manuscript

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

ceph-k1463-tandemrepeats

cloneflow

Pipeline for tracking tumor clone evolution over time and space.

covdist

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

covviz

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

exacresiduals

CCR model

facets-nf

nextflow implementation of the facets data flow.

freebayes-nf

a better freebayes-parallel

ggd-recipes

conda recipes for genomic data

hts-python

pythonic wrapper for htslib

human-rae-manuscript

code used for figure generation and statistical analysis for manuscript

idplot

compare sequences to a shared root reference sequence.

kmertools

mendacity

language-agnostic testing for inheritance models

mendelianerror

probability of mendelian error in trios.

mutator-epistasis-manuscript

pathoscore

pathoscore evaluates variant pathogenicity tools and scores.

preon

Precision Oncology data workflow

proj-mutator-mapping

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

recombinator

regionanalysis

Regional analysis folder

sllobs-biostats

smoove-nf

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

snakemake_tutorial