PROPER 1.16.0 – PROspective Power Evaluation for RNAseq

PROPER 1.16.0

:: DESCRIPTION

PROPER is an R package for power assessment and sample size determination for RNA-seq.

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R

:: DOWNLOAD

   PROPER

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jan 15;31(2):233-41. doi: 10.1093/bioinformatics/btu640.
PROPER: comprehensive power evaluation for differential expression using RNA-seq.
Wu H1, Wang C1, Wu Z

tweeDEseq 1.30.0 – Analyzing RNAseq Count data

tweeDEseq 1.30.0

:: DESCRIPTION

tweeDEseq is an R package for analyzing RNAseq count data. It implements Poisson-Tweedie family of distributions to model count data distribution. This family includes Poisson and Negative Bionomial as particular cases. The testPT test is used to detect genes that are differentially expressed (DE).

::DEVELOPER

Bioinformatic Research Group in Epidemiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 tweeDEseq

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 21;14:254. doi: 10.1186/1471-2105-14-254.
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.
Esnaola M1, Puig P, Gonzalez D, Castelo R, Gonzalez JR.

RNASeqBrowser V2 – A Genome Browser for Strand Specific RNAseq Reads

RNASeqBrowser V2

:: DESCRIPTION

RNASeqBrowser is a visualization tool that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks — all being dynamically built from the BAM file.

::DEVELOPER

Systems Biology of Gene Regulatory Elements

:: SCREENSHOTS

RNASeqBrowser

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

  RNASeqBrowser

:: MORE INFORMATION

Sequgio 0.99.0 – Pre-processing of RNAseq data

Sequgio 0.99.0

:: DESCRIPTION

Sequgio provides an algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn’t assume uniform distribution of count within transcripts.

::DEVELOPER

Stefano Calza, Prof. Yudi Pawitan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • R package

:: DOWNLOAD

 Sequgio

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 15;30(4):506-13. doi: 10.1093/bioinformatics/btt704. Epub 2013 Dec 3.
Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.
Suo C1, Calza S, Salim A, Pawitan Y.

RNASeqR 1.1 – RNAseq Expression Analysis

RNASeqR 1.1

:: DESCRIPTION

 RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries.

::DEVELOPER

Thomas Walk (tom.walk@ars.usda.gov) and Scott Geib (scott.geib@ars.usda.gov)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNASeqR

:: MORE INFORMATION