HuntsmanCancerInstitute/UMIScripts

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Language
Perl
License
Artistic License 2.0
Created about 6 years ago
Updated over 2 years ago

HuntsmanCancerInstitute/UMIScripts

HuntsmanCancerInstitute

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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.

hciR

R package for RNA-seq workflows at HCI

MultiRepMacsChIPSeq

Multiple-replica multiple-condition Macs2 ChIPSeq wrapper

Workflows

Snakemake workflows for best practice genomic analysis

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.

scuir

Single Cell User Interface with R

RBSSeqTools

atac-counter

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