Tag: Allele-specific

LASSIE – Linear Allele-Specific Selection InferencE

LASSIE

:: DESCRIPTION

ASSIE is a statistical model for inferring selection coefficients associated with coding variants in the human genome.

::DEVELOPER

Siepel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

ASSIE

 :: MORE INFORMATION

Citation

Huang YF, Siepel A.
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.
Genome Res. 2019 Aug;29(8):1310-1321. doi: 10.1101/gr.245522.118. Epub 2019 Jun 27. PMID: 31249063; PMCID: PMC6673719.

ALEA 1.2.2 – Allele-specific (AS) Epigenomics Analysis

ALEA 1.2.2

:: DESCRIPTION

ALEA incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 ALEA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 21.
ALEA: a toolbox for allele-specific epigenomics analysis.
Younesy H1, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJ.

ASARP 0.9 – Identification of Allele-Specific Alternative mRNA Processing in RNA-Seq data

ASARP 0.9

:: DESCRIPTION

ASARP is a pipeline for accurate identification of allele-specific alternative mRNA processing

::DEVELOPER

XIAO LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ASARP

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(13):e104. doi: 10.1093/nar/gks280. Epub 2012 Mar 29.
Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
Li G1, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X.