cisASE – Detecting Putative Cis-regulated Allele-specific Expression in RNA Sequencing data

cisASE

:: DESCRIPTION

cisASE is a likelihood-based method for ASE detection at multiple levels(SNV,exon and gene). It takes matched DNA sequencing data as reference to reduce artifacts from technical bias and copy number variation to identify ASE due to cis-acting elements, and it works almost as well for dataset without DNA sequencing.

::DEVELOPER

cisASE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 cisASE

:: MORE INFORMATION

Citation

cisASE: A likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data.
Liu Z, Gui T, Wang Z, Li H, Fu Y, Dong X, Li Y.
Bioinformatics. 2016 Jul 13. pii: btw416.

ASCAT 2.4.3 – Allele-Specific Copy number Analysis of Tumours

ASCAT 2.4.3

:: DESCRIPTION

ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy.

::DEVELOPER

Peter Van Loo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 ASCAT

:: MORE INFORMATION

Citation:

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. Epub 2010 Sep 13.
Allele-specific copy number analysis of tumors.
Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN.

MOCSphaser – Infer Haplotypes composed of Copy Numbers Alleles and SNP Alleles

MOCSphaser

:: DESCRIPTION

MOCSphaser is a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 MOCSphaser

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1645-6. doi: 10.1093/bioinformatics/btn242. Epub 2008 May 20.
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
Kato M1, Nakamura Y, Tsunoda T.

Tandem2 – Automated Microsatellite Allele Binning for Population Genetics Workflows

Tandem2

:: DESCRIPTION

All microsatellite analysis software expects allele sizes given in integer numbers, while allele scoring produces allele sizes with two decimals that are dependent not only on fragment length, but also on fluorescent dye, and GC content. Therefore, allele binning is not a trivial task. Tandem2 fills a gap of the microsatellite workflow by rounding allele sizes to valid integers, depending on the microsatellite repeat units.

::DEVELOPER

Michael Matschiner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 Tandem2

:: MORE INFORMATION

Citation

Matschiner M, Salzburger W (2009)
TANDEM: integrating automated allele binning into genetics and genomics workflows.
Bioinformatics, 25(15), 1982-1983.

ASEQ 1.1.8 – Fast Allele-specific Studies from Next-generation Sequencing data

ASEQ 1.1.8

:: DESCRIPTION

ASEQ (Allele Specific Expression) is a tool to perform gene-level allele-specific expression (ASE) analysis from paired genomic and transcriptomic NGS data without requiring paternal and maternal genome data.

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOSX
  • C Compiler

:: DOWNLOAD

 ASEQ

:: MORE INFORMATION

Citation:

ASEQ: fast allele-specific studies from next-generation sequencing data.
Romanel A, Lago S, Prandi D, Sboner A, Demichelis F.
BMC Med Genomics. 2015 Mar 1;8:9. doi: 10.1186/s12920-015-0084-2.

CalMaTe 0.12.0 – Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

CalMaTe 0.12.0

:: DESCRIPTION

CalMaTe is a multi-array post-processing method of allele-specific copy-number estimates (ASCNs).

::DEVELOPER

Henrik Bengtsson <henrikb at braju.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R

:: DOWNLOAD

 CalMaTe

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1793-4. doi: 10.1093/bioinformatics/bts248. Epub 2012 May 9.
CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.
Ortiz-Estevez M1, Aramburu A, Bengtsson H, Neuvial P, Rubio A.

ABC 1.3 – Allele-specific Binding from ChIP-Seq

ABC 1.3

:: DESCRIPTION

ABC is a computational tool that identifies allele specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs.

::DEVELOPER

ABC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ABC

:: MORE INFORMATION

Citation

ABC: A tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.
Bailey SD, Virtanen C, Haibe-Kains B, Lupien M.
Bioinformatics. 2015 May 20. pii: btv321.

iConvert – Convert Genotype Allele Formats

iConvert

:: DESCRIPTION

The iConvert program allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).

::DEVELOPER

iConvert team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • Python

:: DOWNLOAD

 iConvert

:: MORE INFORMATION

Citation

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A.
BMC Genomics. 2015 Apr 10;16(1):283.

GACT – Genome Build and Allele Definition Conversion Tool

GACT

:: DESCRIPTION

GACT predicts and inter-converts between any of the common SNP allele definitions and between the major genome builds.

::DEVELOPER

Li Laboratory of Human Genetics and Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GACT

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jul 19;15:610. doi: 10.1186/1471-2164-15-610.
GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies.
Sulovari A, Li D

Allim 1.1 – Measuring Allele Specific Gene Expression

Allim 1.1

:: DESCRIPTION

Allim (Allelic imbalance meter) offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • BioPython
  • Java
  • PICARD
  • R
  • SAMTOOLS
  • BedTools

:: DOWNLOAD

 Allim

:: MORE INFORMATION

Citation:

Pandey RV, Franssen SU, Futschik A, Schlötterer C. (2013)
Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.
Mol Ecol Resour. 13(4):740-745.