APPEX 1.0 – Analysis Platform for Identification of Prognostic Gene EXpression Signature in Cancer

APPEX 1.0

:: DESCRIPTION

APPEX is a web-based platform to perform survival analysis, particularly, to support identifying molecular signatures significantly associated with cancer patients’ outcome. APPEX provides various analysis methods to discover genes or any other molecules associated with survival of cancer patients.

::DEVELOPER

Medical Genomics Research Center, KRIBB, Korea.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

APPEX: analysis platform for the identification of prognostic gene expression signatures in cancer.
Kim SK, Kim JH, Yun SJ, Kim WJ, Kim SY.
Bioinformatics. 2014 Aug 4. pii: btu521.

MADGiC 0.2 – a Model-based approach for identifying Driver Genes in Cancer

MADGiC 0.2

:: DESCRIPTION

The R package `MADGiC‘ fits an empirical Bayesian hierarchical model to obtain posterior probabilities that each gene is a driver. The model accounts for (1) frequency of mutation compared to a sophisticated background model that accounts for gene-specific factors in addition to mutation type and nucleotide context, (2) predicted functional impact (in the form of SIFT scores) of each specific change, and (3) positional patterns in mutations that have been deposited into the COSMIC (Catalogue of Somatic Mutations in Cancer) database. Example data from the The Cancer Genome Atlas (TCGA) project ovarian cohort is provided.

::DEVELOPER

Kendziorski Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

 MADGiC

:: MORE INFORMATION

Citation

MADGiC: a model-based approach for identifying driver genes in cancer.
Korthauer KD, Kendziorski C.
Bioinformatics. 2015 Jan 7. pii: btu858.

Chaste 2021.1 – Cancer, Heart and Soft Tissue Environment

Chaste 2021.1

:: DESCRIPTION

Chaste is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling.

::DEVELOPER

Chaste Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

 Chaste

:: MORE INFORMATION

Citation

G.R. Mirams,et al.
Chaste: An Open Source C++ Library for Computational Physiology and Biology.
PLoS Comput Biol 9(3):e1002970, 2013. doi: 10.1371/journal.pcbi.1002970.

LICHeE 1.0 – Multi-sample Cancer Phylogeny Reconstruction

LICHeE 1.0

:: DESCRIPTION

LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution) is a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java Runtime Environment (JRE)

:: DOWNLOAD

 LICHeE

:: MORE INFORMATION

Citation

Fast and scalable inference of multi-sample cancer lineages.
Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S.
Genome Biol. 2015 May 6;16(1):91

Copy Number Explorer 1.3 – Interactive Copy Number Analysis for Cancer Genomics

Copy Number Explorer 1.3

:: DESCRIPTION

Copy Number Explorer is a data mining tool for cancer researchers interested in the structural and copy number changes.

Copy Number Explorer online version

::DEVELOPER

Scott Newman, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • Perl

:: DOWNLOAD

 Copy Number Explorer

:: MORE INFORMATION

Citation

Interactive analysis of large cancer copy number studies with Copy Number Explorer.
Newman S.
Bioinformatics. 2015 May 7. pii: btv298.

Cancerin – Infer Competing Endogenous RNA (ceRNA) interactions in Cancer

Cancerin

:: DESCRIPTION

Cancerin is a tool to infer genome-wide cancer-associated ceRNA interaction network in cancer.

::DEVELOPER

Bozdag Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

Cancerin

:: MORE INFORMATION

Citation

Do D, Bozdag S.
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.
PLoS Comput Biol. 2018 Jul 16;14(7):e1006318. doi: 10.1371/journal.pcbi.1006318. PMID: 30011266; PMCID: PMC6072113.

kronos 2.3.0 – Workflow Assembler for Cancer Genome Analytics and Informatics

kronos 2.3.0

:: DESCRIPTION

Kronos is a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

kronos

:: MORE INFORMATION

Citation

Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.
Kronos: a workflow assembler for genome analytics and informatics.
Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP

xseq 0.2.1 – Assessing Functional Impact on Gene Expression of Mutations in Cancer

xseq 0.2.1

:: DESCRIPTION

Cancer driver mutations control outcomes indirectly through intermediate phenotypes, e.g., gene expression and protein expression. xseq is a probabilistic model which aims to encode the impact of somatic mutations on gene expression profiles.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

xseq

:: MORE INFORMATION

Citation

Nat Commun. 2015 Oct 5;6:8554. doi: 10.1038/ncomms9554.
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
Ding J et al.

TitanCNA v1.17.1 – Analysis of subClonal CNA and LOH in Cancer

TitanCNA v1.17.1

:: DESCRIPTION

TitanCNA is a R/Bioconductor package for analyzing subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in whole genome and exome sequencing of tumours.

::DEVELOPER

The Ha Lab @FredHutch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

TitanCNA

:: MORE INFORMATION

Citation

Ha, G., et al. (2014).
TITAN: Inference of copy number architectures in clonal cell populations from tumour whole genome sequence data.
Genome Research, 24: 1881-1893. (PMID: 25060187)

ReMixT v0.5.18 – Clone-specific Genomic Structure Estimation in Cancer

ReMixT v0.5.18

:: DESCRIPTION

ReMixT is a tool for joint inference of clone specific segment and breakpoint copy number in whole genome sequencing data. The input for the tool is a set of segments, a set of breakpoints predicted from the sequencing data, and normal and tumour bam files. Where multiple tumour samples are available, they can be analyzed jointly for additional benefit.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

ReMixT

:: MORE INFORMATION

Citation

ReMixT: clone-specific genomic structure estimation in cancer.
McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-C?té A, Aparicio S, Sahinalp SC, Shah SP.
Genome Biol. 2017 Jul 27;18(1):140. doi: 10.1186/s13059-017-1267-2.