Tag: Approximation

PRINCE v2.3 – VNTR Copy Number Approximation

PRINCE v2.3

:: DESCRIPTION

PRINCE (Processing Reads to Infer the Number of Copies via Estimation) estimates Variable Number Tandem Repeats (VNTR) copy number from raw next generation sequencing (NGS) data.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • conda

:: DOWNLOAD

PRINCE

:: MORE INFORMATION

Citation

Mehrdad Mansouri and Julian Booth and Margaryta Vityaz and Cedric Chauve and Leonid Chindelevitch
PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats
18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

npGSEA 1.28.0 – Permutation Approximation methods for Gene Set Enrichment Analysis

npGSEA 1.28.0

:: DESCRIPTION

npGSEA  (non-permutation GSEA) calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

::DEVELOPER

Jessica Larson <larson.jess at gmail.com> and Art Owen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 npGSEA

:: MORE INFORMATION

Citation

Moment based gene set tests.
Larson JL, Owen AB.
BMC Bioinformatics. 2015 Apr 28;16(1):132.

PLA – Piecewise-constant and Low-rank Approximation for Multi-sample aCGH Data Analysis

PLA

:: DESCRIPTION

PLA – Piecewise-constant and Low-rank Approximation for Multi-sample aCGH Data Analysis

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 PLA

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Mar 31. [Epub ahead of print]
Piecewise-constant and low-rank approximation for identification of recurrent copy number variations.
Zhou X1, Liu J, Wan X, Yu W.

LRAcluster 1.0 – Low Rank Approximation based Multi-omics Data Clustering

LRAcluster 1.0

:: DESCRIPTION

LRAcluster is a new method to discover molecular subtypes by detecting the low-dimensional intrinsic space of high-dimensional cancer multi-omics data.

::DEVELOPER

Bioinformatics & Intelligent Information Processing Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 LRAcluster

:: MORE INFORMATION

Citation

Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification.
Wu D, Wang D, Zhang MQ, Gu J.
BMC Genomics. 2015 Dec 1;16(1):1022. doi: 10.1186/s12864-015-2223-8.

CLEVER 1.0 – Sequence based Approximation of Protein Energies

CLEVER 1.0

:: DESCRIPTION

CLEVER (Cluster Expansion) is an open-source package that can be used to convert any user-provided energy function into a linear combination of sequence-based terms.

::DEVELOPER

Keating Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 CLEVER

:: MORE INFORMATION

Citation:

Methods Enzymol. 2013;523:171-90. doi: 10.1016/B978-0-12-394292-0.00008-4.
Multistate protein design using CLEVER and CLASSY.
Negron C, Keating AE.

GPASS 1.0 – Genome-wide Poisson Approximation for Statistical Significance

GPASS 1.0

:: DESCRIPTION

GPASS (Genome-wide Poisson Approximation for Statistical Significance) detects SNP disease associations in case control studies, controls FWER and FDR adjusting for dependence/linkage disequilibrium.

::DEVELOPER

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GPASS

:: MORE INFORMATION