SynthEx 1.05 – CNA detection and Tumor Heterogeneity profiling

SynthEx 1.05

:: DESCRIPTION

SynthEx is a comprehensive suite of tools for CNA detection and tumor heterogeneity profiling. It is tailored to cater for the multiple characteristics of different next generation sequencing technologies.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R

:: DOWNLOAD

SynthEx

:: MORE INFORMATION

Citation

Silva GO, Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M.
SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.
Genome Biol. 2017 Apr 8;18(1):66. doi: 10.1186/s13059-017-1193-3. PMID: 28390427; PMCID: PMC5385048.

MixClone 1.1.6 – Mixture Model for Inferring Tumor Subclonal Populations

MixClone 1.1.6

:: DESCRIPTION

MixClone is a comprehensive software package to study the subclonal structures of tumor genomes, including subclonal cellular prevalences estimation, allelic configuration estimation, absolute copy number estimation and a few visualization tools

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/MacOsX
Python

:: DOWNLOAD

MixClone

:: MORE INFORMATION

Citation

BMC Genomics. 2015;16 Suppl 2:S1. doi: 10.1186/1471-2164-16-S2-S1. Epub 2015 Jan 21.
MixClone: a mixture model for inferring tumor subclonal populations.
Li Y, Xie X.

HaDiT 20090702 – Computing and Visualizing Allelic Distortion in Tumor SNP data

HaDiT 20090702

:: DESCRIPTION

HADiT (Haplotype Amplification Distortion in Tumors) is the software written in Java that implements the Amplification Distortion Test (ADT).

::DEVELOPER

Itsik Pe’er Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

HaDiT

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Feb 15;26(4):518-28. doi: 10.1093/bioinformatics/btp694.
Power to detect selective allelic amplification in genome-wide scans of tumor data.
Dewal N, Freedman ML, LaFramboise T, Pe’er I.

BTP 1.0 – Analyzing Intra-tumor Heterogeneity from High-throughput Sequencing data

BTP 1.0

:: DESCRIPTION

BTP (Binary Tree Partition)is a novel combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

BTP

:: MORE INFORMATION

Citation:

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
Hajirasouliha I, Mahmoody A, Raphael BJ.
Bioinformatics. 2014 Jun 15;30(12):i78-86. doi: 10.1093/bioinformatics/btu284.

THetA 0.7 – Tumor Heterogeneity Analysis

THetA 0.7

:: DESCRIPTION

THetA estimates tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsx/WIndows
Java

:: DOWNLOAD

THetA

:: MORE INFORMATION

Citation:

L. Oesper, A. Mahmoody, and B.J. Raphael. (2013)
THetA: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data.
Genome Biology. 14:R80

Shimmer 0.2 – Detection of genetic Alterations in Tumors using Next-generation Sequence data

Shimmer 0.2

:: DESCRIPTION

Shimmer is a software package for the characterization of genetic differences between two very similar samples, e.g., a tumor sample and its matched normal tissue sample.

::DEVELOPER

NHGRI (the National Human Genome Research Institute)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
samtools
R package

:: DOWNLOAD

Shimmer

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jun 15;29(12):1498-503. doi: 10.1093/bioinformatics/btt183. Epub 2013 Apr 24.
Shimmer: detection of genetic alterations in tumors using next-generation sequence data.
Hansen NF, Gartner JJ, Mei L, Samuels Y, Mullikin JC.

TreeClone v1 – Reconstruction of Tumor Subclone Phylogeny Based on Mutation Pairs using Next Generation Sequencing Data

TreeClone v1

:: DESCRIPTION

TreeClone is a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package

:: DOWNLOAD

TreeClone

:: MORE INFORMATION

Citation

[Submitted on 10 Mar 2017 (v1), last revised 25 Oct 2017 (this version, v2)]
TreeClone: Reconstruction of Tumor Subclone Phylogeny Based on Mutation Pairs using Next Generation Sequencing Data
Tianjian Zhou, Subhajit Sengupta, Peter Mueller, Yuan Ji

Epi-Seq 1.0.0 – Predicting Tumor Specific Epitopes from RNA-Seq data

Epi-Seq 1.0.0

:: DESCRIPTION

Epi-Seq is a multi-step bioinformatics analysis pipeline that starts from the raw RNA-Seq tumor reads, and produces a set of predicted tumor-specific expressed epitopes.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux

:: DOWNLOAD

Epi-Seq

:: MORE INFORMATION

GLaD – A Mixed-Membership Model for Heterogenous Tumor Subtype Classification

GLaD

:: DESCRIPTION

GLAD is a mixed-membership classification model that simultaneously learns a sparse biomarker signature for each subtype as well as a distribution over subtypes for each sample.

::DEVELOPER

Flaherty Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
Python

:: DOWNLOAD

GLaD

:: MORE INFORMATION

Citation

GLAD: A mixed-membership model for heterogeneous tumor subtype classification.
Saddiki H, McAuliffe J, Flaherty P.
Bioinformatics. 2014 Sep 29. pii: btu618.

CLONET v2 – CLONality Estimate in Tumors

CLONET v2

:: DESCRIPTION

CLONET is a collection of R scripts which upon estimation of tumor admixture and ploidy infers the clonal hierarchy of genomic aberrations.

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /Windows / MacOSX
R

:: DOWNLOAD

CLONET

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Aug 26;15(8):439. doi: 10.1186/s13059-014-0439-6.
Unraveling the clonal hierarchy of somatic genomic aberrations.
Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F.