Tag: Subset

piMASS 0.9 – Posterior Inference via Model Averaging & Subset Selection

piMASS 0.9

:: DESCRIPTION

piMASS (Posterior inference using Model Averaging and Subset Selection) performs multi-SNP association with disease phenotypes. It can handle all SNPs in the genome simultaneously.piMASS was developed to perform multi-SNP association analysis for large (genome-wide) datasets, although it can also be applied to smaller association analysis data (e.g. candidate genes or regions), and in this case it forms an alternative to the multi-SNP association analysis capabilities of BIMBAM (below). It may also be useful for Bayesian variable selection regression in large-scale problems more generally.

::DEVELOPER

Yongtao Guan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

 piMASS

:: MORE INFORMATION

Citation

Ann. Appl. Stat. Volume 5, Number 3 (2011), 1780-1815.
Bayesian variable selection regression for genome-wide association studies and other large-scale problems
Yongtao Guan and Matthew Stephens

AlignBucket – Identify Optimized Subsets of Protein Sequences for Alignment

AlignBucket

:: DESCRIPTION

AlignBucket is a software for splitting a fasta file into smaller pieces suitable for alignment with BLAST. The constraint used to optimize the result is the required minimum alignment coverage.

::DEVELOPER

Giuseppe Profiti , Piero Fariselli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • g++

:: DOWNLOAD

 AlignBucket

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jul 30. pii: btv451.
AlignBucket: a tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints.
Profiti G, Fariselli P, Casadio R

kSolutionVis 1.4 – Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

kSolutionVis 1.4

:: DESCRIPTION

kSolutionVis is a software for selecting multiple biomarker subsets with similarly effective binary classification performances.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Python

:: DOWNLOAD

kSolutionVis

:: MORE INFORMATION

Citation

J Vis Exp. 2018 Oct 11;(140). doi: 10.3791/57738.
Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances.
Feng X, Wang S, Liu Q, Li H, Liu J, Xu C, Yang W, Shu Y, Zheng W, Yu B, Qi M, Zhou W, Zhou F.

SQN 1.0 – Normalizes based a Subset of Negative Control Probes

SQN 1.0

:: DESCRIPTION

SQN (subset quantile normalization) normalizes based on the distribution of non-specific control features, without restriction on the behavior of specific signals.

::DEVELOPER

Zhijin Wu PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 SQN

:: MORE INFORMATION

Citation

J Comput Biol. 2010 Oct;17(10):1385-95.
Subset quantile normalization using negative control features.
Wu Z, Aryee MJ.

GENERATOR 1.02b – Evaluate and Group Incoherently Annotated Genes into Subsets

GENERATOR 1.02b

:: DESCRIPTION

Generator  (GENElist Research Aimed Theme-discovery executOR)  is a tool to evaluate and group incoherently annotated genes into subsets according to their gene ontology (GO) terms.

::DEVELOPER

Petri Pehkonen ( Petri.Pehkonen@uku.fi)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Generator

:: MORE INFORMATION

Citation:

Pehkonen P, Wong G and Toronen P. (2005)
Theme discovery from gene lists for identification and viewing of multiple functional groups.
BMC Bioinformatics. 2005; 6: 162.

Sub-GSE – Testing Gene Set Enrichment for Subset of Genes

Sub-GSE

:: DESCRIPTION

SubGSE is developed for gene set enrichment analysis.The primary objective of this program is to measure the enrichment of differentially expressed or phenotype associated genes in given gene sets. The input for the program includes the gene expression data of several samples with corresponding phenotypic data (categorical or continuous), and several given gene sets. The program will assess the significance of the enrichment of genes, whose gene expression profiles are associated with the phenotypic data, in each given gene set.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

  SubGSE

:: MORE INFORMATION

Citation

Xiting Yan and Fengzhu Sun
Testing gene set enrichment for subset of genes: Sub-GSE
BMC Bioinformatics 2008, 9:362