naumenko-sa

bioscripts

a bucket of bioinformatics scripts

bioinf_posibnyk_public

cre

excel report generation using data from bcbio variant2 germline pipeline

crt

transcriptome analysis scripts (historically clinical research transcriptome)

crg

clinical reseach genome scripts

umic

barcode counting for inDrops3 single cell RNA-seq protocol

Annovar_Whitelist_Filter_WDL

WDL that runs Annovar and a filtering R Script on the output of Mutect2

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcbio_rnaseq_workflow

bcbio_validation_workflows

A community menagarie of automated variant validations using bcbio and the Common Workflow Language

bcbio_validations

Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

bcbioRNASeq

R package for bcbio RNA-seq analysis.

BGVA_admixture

bioconda-recipes

Conda recipes for the bioconda channel.

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

FusionBenchmarking

Toolkit for benchmarking fusion transcript predictions

hbcABC

Compilation of rmarkdown templates for bioinformatics analysis

hivdrm

Detect HIV Drug Resitant Mutations using amplicon sequencing data

ipython-cluster-helper

Tool to easily start up an IPython cluster on different schedulers.

kent

UCSC Genome Browser source tree. Stable branch: "beta".

knowledgebase

recipes that save time

mamba-feedstock

A conda-smithy repository for mamba.

nextflow-to-icav2-config

R-based helper scripts to generate XML files and modifications to NF configuration files for ICAv2 compatiblity

OptiType

Precision HLA typing from next-generation sequencing data

overmoyer2021_RNAseq_analysis_of_inflammatory_breast_cancer_hbc04141

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

rowe2020_indrop_citeseq_hbc03948

SARS-CoV2_project_GSE149312

scRNA-seq

umis

Tools for processing UMI RNA-tag data