naumenko-sa

Pinned Repositories

bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Language:Python995 86 3.1k353
cloudbiolinux
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
Language:Python257 26 148158
bioinf_posibnyk_public
8 3 01
bioscripts
a bucket of bioinformatics scripts
Language:Perl13 3 14
cre
excel report generation using data from bcbio variant2 germline pipeline
Language:Shell6 4 16
crg
clinical reseach genome scripts
Language:Python3 2 11
crt
transcriptome analysis scripts (historically clinical research transcriptome)
Language:HTML4 3 24
MendelianRNA-seq
Language:Python1 2 01
umic
barcode counting for inDrops3 single cell RNA-seq protocol
Language:C++1 2 00

naumenko-sa's Repositories

naumenko-sa/bioscripts
a bucket of bioinformatics scripts
Language:Perl13 3 14
naumenko-sa/bioinf_posibnyk_public
8 3 01
naumenko-sa/cre
excel report generation using data from bcbio variant2 germline pipeline
Language:Shell6 4 16
naumenko-sa/crt
transcriptome analysis scripts (historically clinical research transcriptome)
Language:HTML4 3 24
naumenko-sa/crg
clinical reseach genome scripts
Language:Python3 2 11
naumenko-sa/umic
barcode counting for inDrops3 single cell RNA-seq protocol
Language:C++1 2 00
naumenko-sa/Annovar_Whitelist_Filter_WDL
WDL that runs Annovar and a filtering R Script on the output of Mutect2
Language:R2 0
naumenko-sa/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Language:Python2 0
naumenko-sa/bcbio_rnaseq_workflow
Language:Shell2 0
naumenko-sa/bcbio_validation_workflows
A community menagarie of automated variant validations using bcbio and the Common Workflow Language
Language:Common Workflow Language2 0
naumenko-sa/bcbio_validations
Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
Language:HTML2 0
naumenko-sa/bcbioRNASeq
R package for bcbio RNA-seq analysis.
Language:R2 0
naumenko-sa/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell2 0
naumenko-sa/cloudbiolinux
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
Language:Python2 0
naumenko-sa/FusionBenchmarking
Toolkit for benchmarking fusion transcript predictions
Language:Perl2 0
naumenko-sa/hbcABC
Compilation of rmarkdown templates for bioinformatics analysis
Language:TeX2 0
naumenko-sa/hivdrm
Detect HIV Drug Resitant Mutations using amplicon sequencing data
Language:Python2 0
naumenko-sa/ipython-cluster-helper
Tool to easily start up an IPython cluster on different schedulers.
Language:Python2 0
naumenko-sa/kent
UCSC Genome Browser source tree. Stable branch: "beta".
naumenko-sa/knowledgebase
recipes that save time
Language:TeX1 0
naumenko-sa/mamba-feedstock
A conda-smithy repository for mamba.
Language:Shell2 0
naumenko-sa/nextflow-to-icav2-config
R-based helper scripts to generate XML files and modifications to NF configuration files for ICAv2 compatiblity
naumenko-sa/OptiType
Precision HLA typing from next-generation sequencing data
Language:Python2 0
naumenko-sa/overmoyer2021_RNAseq_analysis_of_inflammatory_breast_cancer_hbc04141
Language:HTML1 0
naumenko-sa/pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
Language:Python2 0
naumenko-sa/rowe2020_indrop_citeseq_hbc03948
Language:Shell1 0
naumenko-sa/SARS-CoV2_project_GSE149312
naumenko-sa/scRNA-seq
Language:CSS2 0
naumenko-sa/Training-modules
Materials for short, half-day workshops
Language:CSS2 0
naumenko-sa/umis
Tools for processing UMI RNA-tag data
Language:Python2 0