TCLP – Online Cancer Cell Line Catalogue integrating HLA type

TCLP

:: DESCRIPTION

TCLP (TRON CELL LINE PORTAL)is the largest catalog of cancer cell line annotations integrating HLA type, HLA expression, predicted HLA Class I and Class II neo-epitopes, virus, and gene expression.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Scholtalbers J, Boegel S, Bukur T, Byl M, Goerges S, Sorn P, Loewer M, Sahin U, Castle JC:
TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression.
Genome medicine 2015, 7:118.

MUFFINN – Cancer Gene Discovery via Network Analysis of Somatic Mutation data

MUFFINN

:: DESCRIPTION

MUFFINN (MUtations For Functional Impact on Network Neighbors) is a method for prioritizing cancer genes accounting for not only for mutations of individual genes but also those of neighbors in functional networks

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

MUFFINN

:: MORE INFORMATION

Citation

MUFFINN: cancer gene discovery via network analysis of somatic mutation data.
Cho A, Shim JE, Kim E, Supek F, Lehner B, Lee I.
Genome Biol. 2016 Jun 23;17(1):129. doi: 10.1186/s13059-016-0989-x.

BioXpress 3.0 – Gene Expression in Cancer

BioXpress 3.0

:: DESCRIPTION

BioXpress is a gene/miRNA expression and disease association database with expression levels mapped to genes or miRNAs.

::DEVELOPER

High-performance Integrated Virtual Environment (HIVE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.
Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu TJ, Yan C, Zhang H, Mazumder R.
Database (Oxford). 2015 Mar 28;2015. pii: bav019. doi: 10.1093/database/bav019.

BioMuta 4.0 – Single-nucleotide Variations (SNVs) in Cancer

BioMuta 4.0

:: DESCRIPTION

BioMuta is a single-nucleotide variation (SNV) and disease association database where variations are mapped to genomes and RefSeq nucleotide entries, and unified through UniProtKB/Swiss-Prot positional coordinates.

::DEVELOPER

High-performance Integrated Virtual Environment (HIVE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Database (Oxford). 2014 Mar 25;2014:bau022. doi: 10.1093/database/bau022. Print 2014.
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).
Wu TJ1, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R.

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

Shah Lab

:: 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 v0.5.4 – Clone-specific Genomic Structure Estimation in Cancer

ReMixT v0.5.4

:: 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

Shah Lab

:: 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.

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

DriverNet 1.0.0 – Predict Functional Important Driver Genes in Cancer Genome

DriverNet 1.0.0

:: DESCRIPTION

DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

  DriverNet

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R124.
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, Huntsman DG, Caldas C, Aparicio SA, Shah SP.

ApoCanD – Database of Human Apoptotic Proteins in the Context of Cancer

ApoCanD

:: DESCRIPTION

ApoCanD is a database comprises of crucial information of apoptosis proteins in the context of cancer.This database will facilitate the research community working in the field of apoptosis and cancer.

::DEVELOPER

ApoCanD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ApoCanD: Database of human apoptotic proteins in the context of cancer.
Kumar R, Raghava GP.
Sci Rep. 2016 Feb 10;6:20797. doi: 10.1038/srep20797.