Stars
Repository to ZIP Plink2 LD files and have random access
WASP2: High-performance allele-specific analysis pipeline for next-generation sequencing data
Extremely fast Query Engine for DataFrames, written in Rust
Nextflow pipeline to process scDNAseq data
Extremely fast and accurate Nanopore demultiplexing
A battery of methylation tools for PacBio HiFi reads
Python tool for converting files and office documents to Markdown.
Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome
Software to perform multi-ancestry SNP fine-mapping on molecular data
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Workflow for somatic variant calling of long read data
Single-cell analysis in Python. Scales to >100M cells.
Collection of analysis tools for quantitative trait loci
R package for "sum of single effects" regression.
Perform differential expression analysis on cohort-scale single cell datasets using linear mixed models
MMQTL is a statistical package applying meta-analysis to detect multiple QTL signals integrating signals among conditions, with control for population structure and relatedness
Pipeline for processing of single-cell long read DNA data. For example data obtained through 10X-style barcoding of DNA and then sequenced on ONT/PacBio machines.
SV genotyper for long reads with a variation graph
Decima is a Python library to train sequence models on single-cell RNA-seq data.
An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
Guides, FAQ, and how-tos for VSC related activities