HT Genome Analysis Unit

Genome Analysis Unit in the Population Genomic theme

Italy

Pinned Repositories

SCE-VCF
Sample Contamination Estimate from VCF
Language:Nim190
nf-pipeline-regenie
GWAS and rare variants tests at high speed using regenie
Language:Nextflow113
csq_selector
Filter and select variant consequence annotations from snpEff, VEP or bcftools
Language:Nim40
nim-simpleargs
A simple command line argument parser with minimum dependencies
Language:Nim30
DIALOGUE
DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.
Language:R10
tre-containers
Containers recipes for G&H TRE analyses
Language:Dockerfile10
GeNA
Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets
Language:Jupyter Notebook10
rsid_tools
Small utilities to play with dbSNP rsID: annotate rsID for a var or get position for an rsID
Language:Nim10
GEMLI
Fork of GEMLI tool to predict clonal clusters from scRNA expression data
Language:R10
sc_2g_heatmap
Generate heatmap comparing 2 annotation labels in single-cell data
Language:Python10

HT Genome Analysis Unit's Repositories

HTGenomeAnalysisUnit/varcall_training
methods in genomic variant calling training course at Human Technopole
Language:Dockerfile
HTGenomeAnalysisUnit/tre-containers
Containers recipes for G&H TRE analyses
Language:Dockerfile1
HTGenomeAnalysisUnit/DIALOGUE
DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.
Language:R1
HTGenomeAnalysisUnit/variant-annotation-OTG
Tools for annotating variants using OTG data
Language:Python
HTGenomeAnalysisUnit/GeNA
Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets
Language:Jupyter Notebook1
HTGenomeAnalysisUnit/Useful_tips
Tips for various bioinformatic tasks
HTGenomeAnalysisUnit/GEMLI
Fork of GEMLI tool to predict clonal clusters from scRNA expression data
Language:R1
HTGenomeAnalysisUnit/SCE-VCF
Sample Contamination Estimate from VCF
Language:Nim19
HTGenomeAnalysisUnit/csq_selector
Filter and select variant consequence annotations from snpEff, VEP or bcftools
Language:Nim4
HTGenomeAnalysisUnit/nf-pipeline-regenie
GWAS and rare variants tests at high speed using regenie
Language:Nextflow113
HTGenomeAnalysisUnit/id_generator
Random ID generator from a pattern
Language:Python
HTGenomeAnalysisUnit/sc_2g_heatmap
Generate heatmap comparing 2 annotation labels in single-cell data
Language:Python1
HTGenomeAnalysisUnit/rsid_tools
Small utilities to play with dbSNP rsID: annotate rsID for a var or get position for an rsID
Language:Nim1
HTGenomeAnalysisUnit/enformer_variant_score
Support repo to compute and visualize the enformer variant / region scores
Language:Jupyter Notebook
HTGenomeAnalysisUnit/scTranslator
This is a fork of scTranslator prediction model for HT
Language:Jupyter Notebook
HTGenomeAnalysisUnit/LabguruPython
Labguru API via Python
Language:Python
HTGenomeAnalysisUnit/GWAS_reports
Quarto template to generate results report from GWAS or rare variants summary stats
Language:Python
HTGenomeAnalysisUnit/quick_reads_stats
Quick collection of alignment metrics from BAM files
Language:Nim
HTGenomeAnalysisUnit/onek1k_query
small tool to query one1K1K data and retrieve gene expression stratified by genotype
Language:Python
HTGenomeAnalysisUnit/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
Language:Python
HTGenomeAnalysisUnit/nf-genotyping-QC
Pipeline and tutorial for simple genotyping QC
Language:Nextflow
HTGenomeAnalysisUnit/vuepress_doc_template
template to create Vuepress doc and automatic deploy
Language:Shell
HTGenomeAnalysisUnit/ffq
A tool to find sequencing data and metadata from public databases.
HTGenomeAnalysisUnit/shiny_popgen
Shiny apps for teaching Population Genetics
HTGenomeAnalysisUnit/ukb-phasing
A pipeline for phasing UK Biobank whole genome sequence data
HTGenomeAnalysisUnit/nf-pipeline-pgscatalog
The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
HTGenomeAnalysisUnit/nim-simpleargs
A simple command line argument parser with minimum dependencies
Language:Nim3
HTGenomeAnalysisUnit/singleCellTK
Interactively analyze single cell genomic data
HTGenomeAnalysisUnit/multiqc_sctk
MultiQC plugin to parse SCTK QC output as used at HT analysis group
Language:HTML