Pinned Repositories
samtools-view
sam tools view workflow
NGS-PCA
Methods for running PCA on NGS data
jlanej's Repositories
jlanej/samtools-view
sam tools view workflow
jlanej/cigar_swap
Swap in cigar strings from one bam file to another
jlanej/cue
Deep learning framework for SV calling and genotyping
jlanej/docker-bcftools
Docker container for bcftools
jlanej/ExomeDepth
ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
jlanej/hugo-theme-gallery
Gallery Theme for Hugo
jlanej/IGV-VM
Build IGV instance that can take screenshots without a GUI or X11
jlanej/igv-xvfb
IGV with Xvfb
jlanej/lights
jlanej/loma
jlanej/long-read-exp
Experimental utilities for LRS
jlanej/long-read-plot
Exploratory plots for long read sequencing data
jlanej/mimash
jlanej/mochawdl
MoChA WDL pipelines
jlanej/mosdepth-docker
jlanej/NGS-TL
Estimate telomere length (TL) from whole genome sequencing
jlanej/pav
Phased assembly variant caller
jlanej/peddy
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
jlanej/PHESANT
PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank
jlanej/pio
python bio
jlanej/riverway-gis
GIS data for life on river way
jlanej/RUFUS
RUFUS k-mer based genomic variant detection
jlanej/samplot
Plot structural variant signals from many BAMs and CRAMs
jlanej/sandcat
sandcat
jlanej/Sniffles
Structural variation caller using third generation sequencing
jlanej/systemd-ngrok
Automatically start ngrok by systemd
jlanej/truvari
Structural variant toolkit for VCFs
jlanej/TT-Mars
Structural Variants Assessment Based on Haplotype-resolved Assemblies
jlanej/unialigner
jlanej/VAtools
A set of tools to annotate VCF files with expression and readcount data