Tag: SVA

SVA 3.40.0 – Surrogate Variable Analysis

SVA 3.40.0

:: DESCRIPTION

The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment.

::DEVELOPER

 Johnson lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 sva

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Mar 15;28(6):882-3. doi: 10.1093/bioinformatics/bts034. Epub 2012 Jan 17.
The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Leek JT1, Johnson WE, Parker HS, Jaffe AE, Storey JD.

Johnson, WE, Rabinovic, A, and Li, C (2007).
Adjusting batch effects in microarray expression data using Empirical Bayes methods.
Biostatistics 8(1):118-127.

SVA 1.10 – Sequence Variant Analyzer

SVA 1.10

:: DESCRIPTION

SVA is a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits.

::DEVELOPER

Dongliang Ge, PhD.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 SVA

:: MORE INFORMATION

Citation

Ge,Ruzzo, Shianna,He,Pelak, Heinzen, Need, Cirulli, Maia, Dickson, Zhu,Singh, Allen, Goldstein (2011),
“SVA: software for annotating and visualizing sequenced human genomes“,
Bioinformatics, 27:1998-2000