CUT&RUNTools 2.0

Cell Ranger ATAC — 10x Genomics official pipeline for processing single-cell ATAC-seq (scATAC-seq) data from raw FASTQ files to peak-barcode matrices and fragment files. Performs barcode demultiplexin

1 shared topic • 3 shared operations

methylpy — Python pipeline for whole-genome bisulfite sequencing (WGBS) methylation analysis. Trims adapters, aligns with Bowtie2, marks duplicates, and calls cytosine methylation in CpG, CHG, and CHH

1 shared topic • 2 shared operations

ENCODE ChIP-seq pipeline — official ENCODE DCC WDL/Cromwell pipeline for transcription factor (TF) and histone mark ChIP-seq analysis. Handles adapter trimming (Trimmomatic), alignment (Bowtie2/BWA),

3 shared operations

ENCODE DCC ATAC-seq pipeline — ENCODE consortium-standard WDL/Cromwell pipeline (run via Caper) for processing bulk ATAC-seq data from FASTQ through alignment, deduplication, peak calling (MACS2), IDR

3 shared operations

Harmony -- fast and scalable single-cell data integration and batch correction algorithm. Operates on PCA embeddings using iterative soft k-means clustering to remove batch effects while preserving bi

1 shared topic • 1 shared operation