Giotto Suite

Change-O is the Immcantation toolkit for B cell immunoglobulin repertoire analysis. Parse IMGT/IgBLAST V(D)J alignment output into AIRR-format databases with MakeDb.py, cluster sequences into clonotyp

1 shared topic • 2 shared operations

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

1 shared topic • 2 shared operations

Use when preprocessing fMRI data with fMRIPrep. Covers BIDS-compliant preprocessing pipelines, fieldmap correction, ICA-AROMA denoising, confound extraction, surface and volume output spaces, FreeSurf

1 shared topic • 2 shared operations

Giotto Suite — R toolkit for spatial multi-omics analysis at all scales and resolutions. Processes data from Visium, MERFISH, Xenium, CosMx, Slide-seq, CODEX, Stereo-seq, and other spatial technologie

1 shared topic • 2 shared operations

RnBeads — comprehensive R/Bioconductor package for DNA methylation analysis. Supports Illumina Infinium arrays (450K, EPIC/850K), WGBS, RRBS, and other bisulfite sequencing platforms. Key capabilities

1 shared topic • 2 shared operations