YuWang-VUMC

SpaGene

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

singleCellTK

Interactively analyze single cell genomic data

abismal

Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

SCICoNE

Single-cell copy number calling and event history reconstruction.

IMPACT-Pipeline

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

data-science-from-scratch

code for Data Science From Scratch book

gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

gatk3-4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools

SpaGCN

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

snpsea

:bar_chart: Identify cell types and pathways affected by genetic risk loci.

signac

An analytics package for single cell data