tappAS 0.99.15 – Understand the Functional Implications of Alternative Splicing

tappAS 0.99.15

:: DESCRIPTION

tappAS is a Java GUI application for the analysis of RNA-Seq data down to the isoform level.It provides a comprehensive set of data analysis, visualization, filtering, and hoc query tools.It will run on most modern computers, provided they have enough computational resources and storage.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • R package

:: DOWNLOAD

 tappAS

:: MORE INFORMATION

 

SQANTI 1.2 – Structural and Quality Annotation of Novel Transcript Isoforms

SQANTI 1.2

:: DESCRIPTION

SQANTI is a pipeline for the in-depth characterization of isoforms obtained by full-length transcript sequencing, which are commonly returned in a fasta file format without any extra information about gene/transcript annotation or attribute description. SQANTI provides a wide range of descriptors of transcript quality and generates a graphical report to aid in the interpretation of the sequencing results.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • Perl
  • R package

:: DOWNLOAD

 SQANTI

:: MORE INFORMATION

Citation

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.
Genome Res. 2018 Feb 9. doi: 10.1101/gr.222976.117. [Epub ahead of print] Erratum in: Genome Res. 2018 Jul;28(7):1096.
PMID: 29440222

consensusOV 1.4.1 – Gene Expression-based Subtype Classification for High-grade Serous Ovarian Cancer

consensusOV 1.4.1

:: DESCRIPTION

consensusOV implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

  consensusOV

:: MORE INFORMATION

Citation:

Chen GM, Kannan L, Geistlinger L, Kofia V, Waldron L, Haibe-Kains B (2018).
consensusOV: Gene expression-based subtype classification for high-grade serous ovarian cancer. R package version 1.4.1,
http://www.pmgenomics.ca/bhklab/software/consensusOV

MM2S 1.0.5 – Personalized Diagnosis of Medulloblastoma Subtypes Across Patients and Model Systems

MM2S 1.0.5

:: DESCRIPTION

The MM2S (Medullo-Model To Subtypes) classifier stratifies single MB gene expression profiles without reference samples or replicates. The pathway-centric approach facilitates subtype predictions of patient samples, and model systems including cell lines and mouse models.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 MM2S

:: MORE INFORMATION

Citation:

Genomics. 2015 Aug;106(2):96-106. doi: 10.1016/j.ygeno.2015.05.002. Epub 2015 May 12.
Personalized diagnosis of medulloblastoma subtypes across patients and model systems.
Gendoo DM, Smirnov P, Lupien M, Haibe-Kains B

PharmacoGx 1.12.0 – Analysis of large Pharmacogenomic Datasets

PharmacoGx 1.12.0

:: DESCRIPTION

PharmacoGx contains a set of functions to perform large-scale analysis of pharmacogenomic data.

::DEVELOPER

Petr Smirnov, Zhaleh Safikhani, Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 PharmacoGx

:: MORE INFORMATION

Citation

PharmacoGx: An R package for analysis of large pharmacogenomic datasets.
Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DM, Grossman P, Beck AH, Aerts HJ, Lupien M, Goldenberg A, Haibe-Kains B.
Bioinformatics. 2015 Dec 9. pii: btv723

mRMRe 2.0.7 – Parallelized mRMR Ensemble Feature Selection

mRMRe 2.0.7

:: DESCRIPTION

mRMRe contains a set of function to compute mutual information matrices from continuous, categorical and survival variables. It also contains function to perform feature selection with minimum Redundancy, Maximum Relevance (mRMR) and a new ensemble mRMR technique.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 mRMRe

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Sep 15;29(18):2365-8. doi: 10.1093/bioinformatics/btt383. Epub 2013 Jul 3.
mRMRe: an R package for parallelized mRMR ensemble feature selection.
De Jay N, Papillon-Cavanagh S, Olsen C, El-Hachem N, Bontempi G, Haibe-Kains B.

Survcomp 1.32.0 – Performance Assessment and Comparison for Survival Analysis

Survcomp 1.32.0

:: DESCRIPTION

Survcomp is an R package providing functions to assess and to compare the performance of risk prediction (survival) models.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 Survcomp

:: MORE INFORMATION

Citation:

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.
Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B.
Bioinformatics. 2011 Nov 15;27(22):3206-8. doi: 10.1093/bioinformatics/btr511.

Genefu 3.8 – Computation of Gene Expression-Based Signatures in Breast Cancer

Genefu 3.8

:: DESCRIPTION

Genefu contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 Genefu

:: MORE INFORMATION

Citation:

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.
Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B.
Bioinformatics. 2015 Nov 24. pii: btv693.

NOISeq 2.26.0 – Differential Expression in RNA-seq

NOISeq 2.26.0

:: DESCRIPTION

NOISeq is a non-parametric approach for the identification of differentially expressed genes from count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R Package
  • BioConductor

:: DOWNLOAD

 NOISeq

:: MORE INFORMATION

Citation

Tarazona S., García-Alcalde F., Ferrer A., Dopazo J., and Conesa A.
Differential expression in RNA-seq: a matter of depth.
Genome Res. 2011.

PathScore – A Web tool for Identifying Altered Pathways in Cancer data

PathScore

:: DESCRIPTION

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients.

::DEVELOPER

Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • MySQL

:: DOWNLOAD

 PathScore

:: MORE INFORMATION

Citation

PathScore: a web tool for identifying altered pathways in cancer data.
Gaffney SG, Townsend JP.
Bioinformatics. 2016 Aug 8. pii: btw512.