FlipFlop 1.8.0 – Fast Lasso-based Isoform Prediction as a Flow Problem

FlipFlop 1.8.0

:: DESCRIPTION

FlipFlop is a fast method for de novo transcript discovery and abundance estimation from RNA-Seq data.

::DEVELOPER

Centre for Computational Biology

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 FlipFlop

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 9.
Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows.
Bernard E, Jacob L, Mairal J, Vert JP.

lol 1.18.0 – Lots Of Lasso

lol 1.18.0

:: DESCRIPTION

lol contains various optimization methods for matrix-to-matrix Lasso inference, such as cross-validation, randomised lasso, subsampling lasso etc. It is specifically designed for multicollinear predictor variables.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioCOnductor

:: DOWNLOAD

 lol

:: MORE INFORMATION

Citation

A sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes
Y. Yuan, C. Curtis, C. Caldas, F. Markowetz
IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul 20

CCLasso – Correlation Inference for Compositional Data through Lasso

CCLasso

:: DESCRIPTION

CCLasso is a novel method based on least squares with ℓ1 penalty to infer the correlation network for latent variables of compositional data from metagenomic data

::DEVELOPER

Fang Huaying (hyfang@pku.edu.cn) , Minghua Deng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 CCLasso

:: MORE INFORMATION

Citation

CCLasso: Correlation Inference for Compositional Data through Lasso.
Fang H, Huang C, Zhao H, Deng M.
Bioinformatics. 2015 Jun 4. pii: btv349.

msgl 2.0.125.1 – High Dimensional Multiclass Classification using Sparse Group Lasso

msgl 2.0.125.1

:: DESCRIPTION

The R package msgl (multinomial sparse group lasso) fits multinomial models for e.g. multiclass classification with a sparse group lasso penalty.

::DEVELOPER

Niels Richard Hansen 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R

:: DOWNLOAD

 msgl

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1417-23. doi: 10.1093/bioinformatics/btu044. Epub 2014 Jan 24.
Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases.
Vincent M1, Perell K, Nielsen FC, Daugaard G, Hansen NR.

LMM-Lasso – Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction

LMM-Lasso

:: DESCRIPTION

LMM-Lasso is a linear mixed models that allows for both multi-locus mapping and correction for confounding effects.

::DEVELOPER

Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 LMM-Lasso

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 15;29(2):206-14. doi: 10.1093/bioinformatics/bts669.
A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K.

HAPAL – Mapping HAPlotype-haplotype Interactions with Adaptive Lasso

HAPAL

:: DESCRIPTION

HAPAL is an R code for mapping HAPlotype-haplotype interactions with Adaptive Lasso

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 HAPAL

:: MORE INFORMATION

Citation:

BMC Genet. 2010 Aug 27;11:79. doi: 10.1186/1471-2156-11-79.
Mapping haplotype-haplotype interactions with adaptive LASSO.
Li M, Romero R, Fu WJ, Cui Y.

IsoLasso 2.6.1 – A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

IsoLasso 2.6.1

:: DESCRIPTION

IsoLasso is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab
  • C Compiler

:: DOWNLOAD

  IsoLasso

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1693-707. doi: 10.1089/cmb.2011.0171. Epub 2011 Sep 27. IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. Li W1, Feng J, Jiang T.

GGD-Lasso – Graph-regularized dual Lasso for robust eQTL mapping

GGD-Lasso

:: DESCRIPTION

GGD-Lasso (Graph-regularized Dual Lasso) is a robust approach for eQTL mapping.

::DEVELOPER

Wei Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler / MatLab

:: DOWNLOAD

 GGD-Lasso

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i139-i148. doi: 10.1093/bioinformatics/btu293.
Graph-regularized dual Lasso for robust eQTL mapping.
Cheng W, Zhang X, Guo Z, Shi Y, Wang W.

Piet 0.1.0 – DNA CNV Analysis tools based on fused Lasso type of Model

Piet 0.1.0

:: DESCRIPTION

Piet provides some segmentation tools, using fused lasso, group fused lasso and generalized fused lasso (GFL), for analysis of individual or multiple sequences of CNV data.

::DEVELOPER

Piet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • R package

:: DOWNLOAD

 Piet

:: MORE INFORMATION

Citation

Z. Zhang, K. Lange, C. Sabatti (2012)
Reconstructing DNA copy number by joint segmentation of multiple sequences