Projects that are tagged with bioinformatics.
Showing Items 1-20 of 23 on page 1 of 2: 1 2 Next

Logo Weight HMM 1.0

by SongTao - May 27, 2014, 15:29:20 CET [ BibTeX Download ] 361 views, 105 downloads, 1 subscription

About: Discovering short linear protein motif based on selective training of profile hidden Markov models

Changes:

Initial Announcement on mloss.org.


Logo Mr. 1.0

by SongTao - May 27, 2014, 15:20:40 CET [ BibTeX Download ] 275 views, 98 downloads, 1 subscription

About: Discovering short linear protein motif based on selective training of profile hidden Markov models

Changes:

Initial Announcement on mloss.org.


Logo JMLR SHOGUN 3.2.0

by sonne - February 17, 2014, 20:31:36 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 82854 views, 11460 downloads, 5 subscriptions

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About: The SHOGUN machine learning toolbox's focus is on large scale learning methods with focus on Support Vector Machines (SVM), providing interfaces to python, octave, matlab, r and the command line.

Changes:

This is mostly a bugfix release:

Features

  • Fully support python3 now
  • Add mini-batch k-means [Parijat Mazumdar]
  • Add k-means++ [Parijat Mazumdar]
  • Add sub-sequence string kernel [lambday]

Bugfixes

  • Compile fixes for upcoming swig3.0
  • Speedup for gaussian process' apply()
  • Improve unit / integration test checks
  • libbmrm uninitialized memory reads
  • libocas uninitialized memory reads
  • Octave 3.8 compile fixes [Orion Poplawski]
  • Fix java modular compile error [Bjoern Esser]

Logo jackstraw 1.0

by nc - February 1, 2014, 22:53:41 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 960 views, 195 downloads, 1 subscription

About: Estimates statistical significance of association between variables and their principal components (PCs).

Changes:

Initial Announcement on mloss.org.


Logo hapFabia 1.4.2

by hochreit - December 28, 2013, 17:24:29 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 2099 views, 429 downloads, 1 subscription

About: hapFabia is an R package for identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data. It detects 100 times smaller segments than previous methods.

Changes:

o citation update

o plot function improved


Logo FABIA 2.8.0

by hochreit - October 18, 2013, 10:14:57 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 8657 views, 1812 downloads, 1 subscription

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About: FABIA is a biclustering algorithm that clusters rows and columns of a matrix simultaneously. Consequently, members of a row cluster are similar to each other on a subset of columns and, analogously, members of a column cluster are similar to each other on a subset of rows. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. Applications include detection of transcriptional modules in gene expression data and identification of haplotypes/>identity by descent< consisting of rare variants obtained by next generation sequencing.

Changes:

CHANGES IN VERSION 2.8.0

NEW FEATURES

o rescaling of lapla
o extractPlot does not plot sorted matrices

CHANGES IN VERSION 2.4.0

o spfabia bugfixes

CHANGES IN VERSION 2.3.1

NEW FEATURES

o Getters and setters for class Factorization

2.0.0:

  • spfabia: fabia for a sparse data matrix (in sparse matrix format) and sparse vector/matrix computations in the code to speed up computations. spfabia applications: (a) detecting >identity by descent< in next generation sequencing data with rare variants, (b) detecting >shared haplotypes< in disease studies based on next generation sequencing data with rare variants;
  • fabia for non-negative factorization (parameter: non_negative);
  • changed to C and removed dependencies to Rcpp;
  • improved update for lambda (alpha should be smaller, e.g. 0.03);
  • introduced maximal number of row elements (lL);
  • introduced cycle bL when upper bounds nL or lL are effective;
  • reduced computational complexity;
  • bug fixes: (a) update formula for lambda: tighter approximation, (b) corrected inverse of the conditional covariance matrix of z;

1.4.0:

  • New option nL: maximal number of biclusters per row element;
  • Sort biclusters according to information content;
  • Improved and extended preprocessing;
  • Update to R2.13

Logo JMLR Jstacs 2.1

by keili - June 3, 2013, 07:32:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 13672 views, 3226 downloads, 2 subscriptions

About: A Java framework for statistical analysis and classification of biological sequences

Changes:

New classes:

  • MultipleIterationsCondition: Requires another TerminationCondition to fail a contiguous, specified number of times
  • ClassifierFactory: Allows for creating standard classifiers
  • SeqLogoPlotter: Plot PNG sequence logos from within Jstacs
  • MultivariateGaussianEmission: Multivariate Gaussian emission density for a Hidden Markov Model
  • MEManager: Maximum entropy model

New features and improvements:

  • Alignment: Added free shift alignment
  • PerformanceMeasure and sub-classes: Extension to weighted test data
  • AbstractClassifier, ClassifierAssessment and sub-classes: Adaption to weighted PerformanceMeasures
  • DNAAlphabet: Parser speed-up
  • PFMComparator: Extension to PFM from other sources/databases
  • ToolBox: New convenience methods for computing several statistics (e.g., median, correlation)
  • SignificantMotifOccurrencesFinder: New methods for computing PWMs and statistics from predictions
  • SequenceScore and sub-classes: New method toString(NumberFormat)
  • DataSet: Adaption to weighted data, e.g., partitioning
  • REnvironment: Changed several methods from String to CharSequence

Restructuring:

  • changed MultiDimensionalSequenceWrapperDiffSM to MultiDimensionalSequenceWrapperDiffSS

Several minor new features, bug fixes, and code cleanups


Logo BCILAB 1.0-beta

by chkothe - January 6, 2012, 23:47:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3051 views, 618 downloads, 1 subscription

About: MATLAB toolbox for advanced Brain-Computer Interface (BCI) research.

Changes:

Initial Announcement on mloss.org.


Logo NetPro 1.1.17

by lml - January 25, 2011, 19:02:53 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3191 views, 758 downloads, 1 subscription

About: Tools for functional network analysis.

Changes:

Initial Announcement on mloss.org.


Logo Epistatic MAP Imputation 1.1

by colm - November 25, 2010, 21:01:10 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 2607 views, 625 downloads, 1 subscription

About: Epistatic miniarray profiles (E-MAPs) are a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values - up to 35% - that can reduce the effectiveness of some data analysis techniques and prevent the use of others. This project contains nearest neighbor based tools for the imputation and prediction of these missing values. The code is implemented in Python and uses a nearest neighbor based approach. Two variants are used - a simple weighted nearest neighbors, and a local least squares based regression.

Changes:

Initial Announcement on mloss.org.


Logo LSTM for biological sequence analysis 1.0

by mhex - July 28, 2010, 16:32:29 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5281 views, 1235 downloads, 1 subscription

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About: Implementation of LSTM for biological sequence analysis (classification, regression, motif discovery, remote homology detection). Additionally a LSTM as logistic regression with spectrum kernel is included.

Changes:

Spectrum LSTM package included


Logo asp 0.3

by sonne - May 7, 2010, 10:25:39 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 7302 views, 1441 downloads, 1 subscription

About: Accurate splice site predictor for a variety of genomes.

Changes:

Asp now supports three formats:

-g fname for gff format

-s fname for spf format

-b dir for a binary format compatible with mGene.

And a new switch

-t which switches on a sigmoid-based transformation of the svm scores to get scores between 0 and 1.


Logo Dependency modeling toolbox 0.2

by lml - April 30, 2010, 14:38:45 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 6885 views, 1058 downloads, 1 subscription

About: Investigation of dependencies between multiple data sources allows the discovery of regularities and interactions that are not seen in individual data sets. The demand for such methods is increasing with the availability and size of co-occurring observations in computational biology, open data initiatives, and in other domains. We provide practical, open access implementations of general-purpose algorithms that help to realize the full potential of these information sources.

Changes:

Three independent modules (drCCA, pint, MultiWayCCA) have been added.


Logo svmPRAT 1.0

by rangwala - December 28, 2009, 00:27:03 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3635 views, 897 downloads, 1 subscription

About: BACKGROUND:Over the last decade several prediction methods have been developed for determining the structural and functional properties of individual protein residues using sequence and sequence-derived information. Most of these methods are based on support vector machines as they provide accurate and generalizable prediction models. RESULTS:We present a general purpose protein residue annotation toolkit (svmPRAT) to allow biologists to formulate residue-wise prediction problems. svmPRAT formulates the annotation problem as a classification or regression problem using support vector machines. One of the key features of svmPRAT is its ease of use in incorporating any user-provided information in the form of feature matrices. For every residue svmPRAT captures local information around the reside to create fixed length feature vectors. svmPRAT implements accurate and fast kernel functions, and also introduces a flexible window-based encoding scheme that accurately captures signals and pattern for training eective predictive models. CONCLUSIONS:In this work we evaluate svmPRAT on several classification and regression problems including disorder prediction, residue-wise contact order estimation, DNA-binding site prediction, and local structure alphabet prediction. svmPRAT has also been used for the development of state-of-the-art transmembrane helix prediction method called TOPTMH, and secondary structure prediction method called YASSPP. This toolkit developed provides practitioners an efficient and easy-to-use tool for a wide variety of annotation problems. Availability: http://www.cs.gmu.edu/~mlbio/svmprat/

Changes:

Initial Announcement on mloss.org.


Logo seqan 1.2

by sonne - November 2, 2009, 14:54:08 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5934 views, 1138 downloads, 1 subscription

About: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Changes:
  • 5 more applications, i.e. DFI, MicroRazerS, PairAlign, SeqCons, TreeRecon
  • stable release of RazerS supporting paired-end read mapping and configurable sensitivity
  • new alignment algorithms, e.g. banded, configurable alignments (overlap, semi-global, ...)
  • realignment algorithm
  • NGS data structures and formats, e.g. SAM, Amos, ...
  • new alphabets, e.g. Dna with base call qualities, profile characters
  • auxiliary data structures and algorithms, e.g. double ended queue, command line parser
  • positional scores
  • CMake support

Logo Easysvm 0.3

by gxr - June 25, 2009, 18:33:04 CET [ Project Homepage BibTeX Download ] 7941 views, 1505 downloads, 1 subscription

About: The Easysvm package provides a set of tools based on the Shogun toolbox allowing to train and test SVMs in a simple way.

Changes:

Fixes for shogun 0.7.3.


Logo arts 0.2

by sonne - May 25, 2009, 09:56:31 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 4295 views, 895 downloads, 1 subscription

About: ARTS is an accurate predictor for Transcription Start Sites (TSS).

Changes:

Initial Announcement on mloss.org.


Logo Spike train feature extraction by Bayesian binning 0.1

by dendres - September 24, 2008, 16:19:14 CET [ BibTeX BibTeX for corresponding Paper Download ] 5378 views, 1276 downloads, 0 comments, 1 subscription

About: *binsdfc* is a command line implementation of the algorithm described in [Endres,Oram,Schindelin,Foldiak:*Bayesian binning beats approximate alternatives: estimating peri-stimulus time histograms*, [...]

Changes:

Changed build system from automake to cmake. Moved download page to www.compsens.uni-tuebingen.de


Logo Nested Effects Models 2.4.0

by florian - July 8, 2008, 00:05:59 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5115 views, 1321 downloads, 1 subscription

About: Nested Effects Models (NEMs) are a class of directed graphical models originally introduced to analyze the effects of gene perturbation screens with high-dimensional phenotypes. In contrast to other [...]

Changes:

Initial Announcement on mloss.org.


Logo Sleipnir 1.0

by chuttenh - June 30, 2008, 03:22:19 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5530 views, 1229 downloads, 1 subscription

About: The Sleipnir C++ library implements a variety of machine learning and data manipulation algorithms focusing on heterogeneous data integration and efficiency for large biological data collections.

Changes:

Initial Announcement on mloss.org.


Showing Items 1-20 of 23 on page 1 of 2: 1 2 Next