:: DESCRIPTION
TumorHPD is a web server for predicting and designing tumor homing peptides. This server is extremely useful for the researchers working in the field of therapeutic peptides.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Computational approach for designing tumor homing peptides.
Sharma A, Kapoor P, Gautam A, Chaudhary K, Kumar R, Chauhan JS, Tyagi A, Raghava GP.
Sci Rep. 2013;3:1607. doi: 10.1038/srep01607.
:: DESCRIPTION
BubbleTree is a framework to characterize the tumor clonality using next generation sequencing (NGS) data.
::DEVELOPER
Wei Zhu <zhuw at medimmune.com>, Michael Kuziora <kuzioram at medimmune.com>, Todd Creasy <creasyt at medimmune.com>, Brandon Higgs <higgsb at medimmune.com>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data.
Zhu W, Kuziora M, Creasy T, Lai Z, Morehouse C, Guo X, Sebastian Y, Shen D, Huang J, Dry JR, Xue F, Jiang L, Yao Y, Higgs BW.
Nucleic Acids Res. 2015 Nov 17. pii: gkv1102
:: DESCRIPTION
The R package ‘contamDE’ conducts differential expression (DE) analysis using high throughput next-generation RNA-seq read count data generated from contaminated tumor samples that are either matched or unmatched with normal samples, which estimates the proportion of pure tumor cells in each contaminated tumor sample, and provides tumor vs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
contamDE: Differential expression analysis of RNA-seq data for contaminated tumor samples.
Shen Q, Hu J, Jiang N, Hu X, Luo Z, Zhang H.
Bioinformatics. 2015 Nov 9. pii: btv657.
:: DESCRIPTION
This program suite consists of 4 PERL programs made to identify and remove potential false positive somatic variants caused by FFPE (formalin-fixed paraffin-embedded) DNA damage on next-generation sequencing data.
::DEVELOPER
the Division of Genome Information Sciences, UCSD
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2012 Aug;40(14):e107. Epub 2012 Apr 6.
Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens.
Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA, Harismendy O, Frazer KA.
:: DESCRIPTION
TRUP is a pipeline designed for analyzing RNA-seq data from Tumor samples.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
DiNAMIC (Discovering Copy Number Aberrations Manifested In Cancer) is a novel method for assessing the statistical significance of recurrent copy number aberrations. In contrast to competing procedures, the testing procedure underlying DiNAMIC is carefully motivated, and employs a novel cyclic permutation scheme. Extensive simulation studies show that DiNAMIC controls false positive discoveries in a variety of realistic scenarios.
::DEVELOPER
V. Walter, A.B. Nobel, and F.A. Wright
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
V. Walter, A.B. Nobel, and F.A. Wright
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors
Bioinformatics (2011) 27 (5): 678-685.
