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10xranger-nf

A Nextflow wrapper for 10X Cellranger and spaceranger to wrangle the 10,000+ output files per sample

alademux

A la carte demultiplexing with python

atac-counter

Alternative counting for 10x Genomics single cell ATAC-seq data

autoaligner

autoanalysis

AutoAnalysis orchestrates auto analysis of sequencing files in GNomEx Experiment using two different daemons running on HCI and CHPC servers. This is a custom toolkit for internal use at the University of Utah.

awsapps

Genomic data focused toolkit for working with Amazon AWS S3 and EC2

bcode

biominerqt

The BioMiner Query Tool is a multi-omic, cross species, web-app that ingests ChIP/RNA/Bisulfite/Variant-Seq analysis and enables users to perform iterative searches to identify records based on region or gene name.

gquery

GQuery is a software tool for rapidly querying large numbers of bgzip compressed, tabix indexed genomic data files e.g. vcf, maf, bed, bedGraph, etc. from multiple species with different genome builds without the need to develop, debug, and maintain custom file parsers. Search for particular germline or somatic mutations, copy number changes, differentially expressed genes, epigenetic marks, anything that can be associated with genomic coordinates. Just point the GQuery indexer at a collection of tabix indexed files and then run either the GQuery command line app or the web API to search them. GQuery is built using a fast, multi-threaded, genomic range search engine with extensive junit testing.

hci-bio-repository

internal scripts for bio-repo management

hci-demux

hcir

R package for RNA-seq workflows at HCI

hcir2

Extra functions for hciR package

hcirdata

Datasets for hciR package

hcirscripts

R scripts for hciR package

multirepmacschipseq

Multiple-replica multiple-condition Macs2 ChIPSeq wrapper

mutationscreen

nextflowworkflow

rbsseqtools

sb-apps

Seven Bridges application tools and workflows

sbapps

Tools for working with the Seven Bridges bioinformatics platform.

scuir

Single Cell User Interface with R

subjectmatchmaker

Master human subject ID generator and matcher based on PHI keys - name, dob, gender, mrn

umiscripts

Simple scripts for handling Unique Molecular Indexes in Fastq and Bam files

useq

180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.

workflows

Snakemake workflows for best practice genomic analysis