Tag: Heterogeneity

SpliceHetero – Measuring Spliceomic Intratumor Heterogeneity from bulk-tumor RNA-seq

SpliceHetero

:: DESCRIPTION

SpliceHetero is a novel computational method to measure spliceome level intra-tumor heterogeneity (sITH) in breast cancer.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SpliceHetero

:: MORE INFORMATION

Citation

Kim M, Lee S, Lim S, Kim S.
SpliceHetero: An information theoretic approach for measuring spliceomic intratumor heterogeneity from bulk tumor RNA-seq.
PLoS One. 2019 Oct 23;14(10):e0223520. doi: 10.1371/journal.pone.0223520. PMID: 31644551; PMCID: PMC6808416.

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.

HIPPO 1.5.0 – Heterogeneity Inspired pre-processing Tool

HIPPO 1.5.0

:: DESCRIPTION

HIPPO is a novel framework that leverages zero proportions to explain cellular heterogeneity and integrates feature selection with iterative clustering.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R 

:: DOWNLOAD

HIPPO

:: MORE INFORMATION

Citation

Kim TH, Zhou X, Chen M.
Demystifying “drop-outs” in single-cell UMI data.
Genome Biol. 2020 Aug 6;21(1):196. doi: 10.1186/s13059-020-02096-y. PMID: 32762710; PMCID: PMC7412673.

Homo 2.0 – Surveying and Visualizing Compositional Heterogeneity across Aligned Sequence data

Homo 2.0

:: DESCRIPTION

Homo is a program written to allow its users to check whether aligned nucleotide or amino acid sequences are consistent with evolution under globally stationary, reversible, and homogeneous (SRH) conditions.

::DEVELOPER

CSIRO Transformational Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

Homo

:: MORE INFORMATION

Citation

Jermiin L.S., Lovell D.R., Misof B., Robinson J. 2020.
Software for detecting heterogeneous evolutionary processes across aligned
sequence data. (in review).
https://www.biorxiv.org/content/10.1101/828996v1

MismatchHetMutRate – Perform Mismatch Analyses allowing for Heterogeneity of Mutation Rates

MismatchHetMutRate

:: DESCRIPTION

MismatchHetMutRate is a series of programs to perform mismatch analyses allowing for heterogeneity of mutation rates.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MismatchHetMutRate

:: MORE INFORMATION

Citation

Schneider, S. and L. Excoffier (1999)
Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites. Application to human mitochondrial DNA.
Genetics 152: 1079-1089.

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.

SHEAR 1.1.2 – Sample Heterogeneity Estimation and Assembly by Reference

SHEAR 1.1.2

:: DESCRIPTION

SHEAR is a tool for next-generation sequencing data analysis that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis.

::DEVELOPER

Hwang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SHEAR

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jan 29;15:84. doi: 10.1186/1471-2164-15-84.
SHEAR: sample heterogeneity estimation and assembly by reference.
Landman SR, Hwang TH1, Silverstein KA, Li Y, Dehm SM, Steinbach M, Kumar V.

DNA Slider – Tests Heterogeneity in the Polymorphism-to-divergence Ratio among Different Regions of a Gene

DNA Slider

:: DESCRIPTION

DNA Slider is program for performing four significance tests of heterogeneity in the ratio of polymorphic sites to fixed differences in DNA sequence data.

::DEVELOPER

John H. McDonald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 DNA Slider

:: MORE INFORMATION

Citation

McDonald, J.H. 1998.
Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence.
Molecular Biology and Evolution 15: 377-384.

SeqVis 1.5 – Visualization of Compositional Heterogeneity in Large Alignments of Nucleotides

SeqVis 1.5

:: DESCRIPTION

SeqVis is a stand-alone, platform-independent Java application developed with the aim to facilitate analysis and 3D visualization of compositional heterogeneity in species-rich alignments of nucleotide sequences. Each sequence is represented by a dot in a tetrahedron plot (i.e., an extension of the de Finetti), where the position of the dot depends uniquely on the nucleotide content of that sequence. Sequences that are compositionally different will appear as dots found in different areas within the tetrahedron. SeqVis also allows users to analyse their data set using, for example, the useful matched-pairs test of symmetry (Ababneh et al. 2006)

::DEVELOPER

Lars S. Jermiin

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOs / Linux / Unix
  • Java

:: DOWNLOAD

  SeqVis

:: MORE INFORMATION

Citation:

Ho JWK, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS (2006).
SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides.
Bioinformatics 22, 2162-2163.