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aneufinder

Find CNVs in single cell sequencing data.

apeinversion_paper

A set of supplementary files for the study: "Recurrent inversion toggling and great ape genome evolution".

breakpointr

R Package for breakpoint detection in single cell Strand-seq data.

breakpointr_paper

Supplementary files for the study "breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data"

breakpointrdata

crosslinkr

This package is currently under the development.

diploidassembly_paper

Under development

ggnucfreak

A tool to visualize nucleotide and base modification frequencies in aligned sequencing reads.

hapscelocator

R package to detect SCE breakpoints in yeast Strand-seq data

hicer

Set of utilities to process Hi-C data

integrativephasingpaper

Supplementary files for the study "Dense and accurate whole-chromosome haplotyping of individual genomes"

primatr

An R package of useful functions to process and analyze Strand-seq data.

rtoolbox

Various R functions for genomic data processing.

saarclust

saarclust2

TODO

saarclustexampledata

Example data for SaaRclust package

shiny_hackathon

strandphase

Set of Perl scripts to assemble hapotypes from Strand-seq data

strandphaser

R Package for phasing of single cell Strand-seq data

svbyeye

t2t-chm13_inversion_polymorphism_paper

Supplementary code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.