🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips

GeneDMRs is an R package to detect the differentially methylated regions based on genes, gene body, CpG islands and gene body interacted with CpG island features.

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read…

Battenberg R package for subclonal copynumber estimation

deep learning-inspired explainable sequence model for transcription initiation

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

ClairS - a deep-learning method for long-read somatic small variant calling

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Mutational Signatures extraction - Pediatric cancers

A robust framework to filter cell-free droplets in scRNA-seq data

Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data

Clean up single-cell data

CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.

Imputation of missing values of a matrix or data.frame using iterative prediction model

a tool for inferring species tree from sequencing reads

Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics