iCAGES 1.0.2 – Prioritizing Cancer driver Genes

iCAGES 1.0.2

:: DESCRIPTION

iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patient. Given his/her genomic mutation information, iCAGES can accurately prioritize a list of candidate cancer driver genes.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 iCAGES

:: MORE INFORMATION

Citation

Dong C, Guo Y, Yang H, He Z, Liu X, Wang K.
iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes.
Genome Med. 2016 Dec 22;8(1):135. doi: 10.1186/s13073-016-0390-0. PMID: 28007024; PMCID: PMC5180414.

MethylMix 2.20.0 – Identifying DNA Methylation Driven Genes

MethylMix 2.20.0

:: DESCRIPTION

MethylMix is an algorithm implemented in R to identify disease specific hyper and hypomethylated genes.

::DEVELOPER

 Gevaert lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows /MacOsX
  • R BioConductor / Matlab

:: DOWNLOAD

 MethylMix

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jan 20. pii: btv020. [Epub ahead of print]
MethylMix: an R package for identifying DNA methylation driven genes.
Gevaert O

OEFinder 0.0.2 – Identify Ordering Effect Genes in Single Cell RNA-seq data

OEFinder 0.0.2

:: DESCRIPTION

OEFinder is a user interface to identify and visualize ordering effects in single-cell RNA-seq data.

::DEVELOPER

Ning Leng

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 OEFinder

:: MORE INFORMATION

Citation

OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data.
Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R.
Bioinformatics. 2016 Jan 6. pii: btw004.

Annokey – Gene-based Search for Key-terms in NCBI Gene Database and Associated PubMed Abstracts

Annokey

:: DESCRIPTION

Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 Annokey

:: MORE INFORMATION

Pan-Tetris 0.9 – Interactive Pan-genome Visualization

Pan-Tetris 0.9

:: DESCRIPTION

Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game.

::DEVELOPER

Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOS / WIndows
  • Java

:: DOWNLOAD

 Pan-Tetris

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015;16 Suppl 11:S3. doi: 10.1186/1471-2105-16-S11-S3. Epub 2015 Aug 13.
Pan-Tetris: an interactive visualisation for Pan-genomes.
Hennig A, Bernhardt J, Nieselt K.

GCUA 1.2 – Evaluate Codon Usage in a set of Genes

GCUA 1.2

:: DESCRIPTION

GCUA (General Codon Usage Analysis) is designed to perform various tasks that are of use for evaluating codon usage in a set of genes.  You can get it to do some simple things like calculate the number of observations of a particular codon in a gene.  Or you can do the same thing for the combined dataset.  You can also look at amino acid usage frequencies (again for each gene or for the dataset as a whole).  The program also produces a distance matrix based on the similarity of codon usage in genes.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

GCUA

:: MORE INFORMATION

Citation:

McInerney, J.O. (1998).
GCUA (General Codon Usage Analysis).
Bioinformatics: 14 (4) 372-373.

simDEF – Definition-based Semantic Similarity Measure of GO Terms for Functional Similarity Analysis of Genes

simDEF

:: DESCRIPTION

simDEF is an efficient method for measuring semantic similarity of GO terms using their GO definitions.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  simDEF

:: MORE INFORMATION

Citation:

simDEF: Definition-based Semantic Similarity Measure of Gene Ontology Terms for Functional Similarity Analysis of Genes.
Pesaranghader A, Matwin S, Sokolova M, Beiko RG.
Bioinformatics. 2015 Dec 26. pii: btv755.

isONclust 0.0.4 – de novo Clustering of long Transcript Reads into Genes

isONclust 0.0.4

:: DESCRIPTION

isONclust is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

isONclust

:: MORE INFORMATION

Citation

Kristoffer Sahlin, Paul Medvedev (2019)
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm“,
RECOMB 2019

gespeR 0.99.5 – Gene Specific Phenotype Estimator

gespeR 0.99.5

:: DESCRIPTION

gespeR estimates gene-specific phenotypes from off-target confounded RNAi screens. Observed phenotype for a specfic siRNA is modeled as a linear combination of gene-specific phenotypes from the on- and all off-target genes.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

 gespeR

:: MORE INFORMATION

Citation

Fabian Schmich, Ewa Szczurek, Saskia Kreibich, Sabrina Dilling, Daniel Andritschke, Alain Casanova, Shyan Huey Low, Simone Eicher, Simone Muntwiler, Mario Emmenlauer, Pauli Ramo, Raquel Conde-Alvarez, Christian von Mering, Wolf-Dietrich Hardt, Christoph Dehio and Niko Beerenwinkel.
gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens
Genome Biology, 2015.