Epiclomal

Use when working with batchelor — the Bioconductor R package for batch correction of single-cell RNA-seq data. Removes batch effects using mutual nearest neighbours (fastMNN, mnnCorrect), linear resca

2 shared topics • 1 shared operation

CHESS (Comparison of Hi-C Experiments using Structural Similarity) — Python command-line tool for quantitative comparison and automatic feature extraction of chromatin contact data using the structura

2 shared topics • 1 shared operation

DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

2 shared topics • 1 shared operation

IsoSeq — PacBio official full-length isoform sequencing pipeline for generating high-quality, full-length cDNA transcripts from PacBio SMRT/HiFi reads. Converts raw CCS reads through primer removal (l

2 shared topics • 1 shared operation

SEACells — single-cell metacell identification using kernel archetypal analysis. Aggregates highly similar single cells into metacells that preserve transcriptional and epigenomic heterogeneity while

2 shared topics • 1 shared operation