Software Updates

DROP

(Detection of RNA Outlier Pipeline) pipeline to find aberrant gene expression events in RNA sequencing data.

Cell Ranger

a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

scan2

Genotyper for somatic SNV and indel discovery in PTA-amplified single cells.

TreeTime

TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies.

PhaseDel

PhaseDel is a Java-based variant caller designed for detecting somatic deletions from high-coverage (~30x) single-cell whole-genome sequencing (scWGS) data.

FreeSurfer

is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.

CRKIT

CRKIT (Computational Radiology Kit) is a collection of algorithms and image processing tools developed by the Computational Radiology Laboratory team

LiRA

LiRA (Linked Read Analysis) is a computational tool for removing amplification artifacts from single-cell DNA sequencing data and estimating mutation rates in single cells.

AbundanceBin

AbundanceBin is an abundance-based tool for binning metagenomic sequences.

quip

Quip compresses next-generation sequencing data with extreme prejudice.