Serhiy Naumenko's repositories
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
knowledgebase
recipes that save time
hivdrm
Detect HIV Drug Resitant Mutations using amplicon sequencing data
bioscripts
a bucket of bioinformatics scripts
nextflow-to-icav2-config
R-based helper scripts to generate XML files and modifications to NF configuration files for ICAv2 compatiblity
cloudbiolinux
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
Annovar_Whitelist_Filter_WDL
WDL that runs Annovar and a filtering R Script on the output of Mutect2
bioconda-recipes
Conda recipes for the bioconda channel.
bcbioRNASeq
R package for bcbio RNA-seq analysis.
bcbio_validation_workflows
A community menagarie of automated variant validations using bcbio and the Common Workflow Language
ipython-cluster-helper
Tool to easily start up an IPython cluster on different schedulers.
OptiType
Precision HLA typing from next-generation sequencing data
FusionBenchmarking
Toolkit for benchmarking fusion transcript predictions
pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
umis
Tools for processing UMI RNA-tag data
mamba-feedstock
A conda-smithy repository for mamba.
hbcABC
Compilation of rmarkdown templates for bioinformatics analysis
bcbio_validations
Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
Training-modules
Materials for short, half-day workshops