Tag: ABACUS

Abacus 20160720 – Extracting Spectral Counts from MS/MS Data Sets.

Abacus 20160720

:: DESCRIPTION

Abacus is a tool for extracting adjusted spectral counts from the result XML files generated by the Trans-Proteomic Pipeline (TPP). Abacus outputs a tab-delimited file that can be used for label-free quantification or simply viewing proteomics results across multiple experimental runs.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOs
  • Java

:: DOWNLOAD

Abacus 

:: MORE INFORMATION

Citation:

Proteomics. 2011 Apr;11(7):1340-5. doi: 10.1002/pmic.201000650. Epub 2011 Feb 17.
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.
Fermin D, Basrur V, Yocum AK, Nesvizhskii AI.

ABACUS 1.0 – Identify SNPs Significantly Associated with a Disease within predefined sets of SNPs

ABACUS 1.0

:: DESCRIPTION

ABACUS (Algorithm based on a BivAriate CUmulative Statistic) is designed to identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions.Applied to a whole SNP dataset, ABACUS gives as output a list of SNP-sets associated with the disease and, for each SNP-set, the list of significant SNPs. ABACUS is robust to the concurrent presence of SNPs with protective and detrimental effects and of common and rare variants; moreover it is powerful even when few SNPs in the SNP-set are associated with the phenotype.

::DEVELOPER

SYSTEMS BIOLOGY AND BIOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • R package

:: DOWNLOAD

 ABACUS

:: MORE INFORMATION

Citation

Di Camillo B, Sambo F, Toffolo G, Cobelli C.
ABACUS: an entropy based cumulative bivariate statistic robust to rare variants and different direction of genotype effect .
Bioinformatics. 2014 Feb 1;30(3):384-91. doi: 10.1093/bioinformatics/btt697.