Showing 25 open source projects for "python feature selection"

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  • 1

    DataPrep

    Python-based data preprocessing tool

    DataPrep v0.2 is a Tkinter-based GUI application/tool designed to assist users in data preprocessing, multicollinearity removal, and feature selection for a wide range of applications in Cheminformatics, Bioinformatics, Data Analysis, Feature Selection, Molecular Modeling, Machine Learning, and Quantitative-structure-property relationship (QSPR) studies. It includes functionality to load, process, and save datasets with support for different preprocessing & multicollinearity removal strategies...
    Downloads: 2 This Week
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  • 2

    MutaNET

    NGS Pipeline and Automated Mutation Analysis

    MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance.
    Downloads: 1 This Week
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  • 3
    raxmlGUI
    RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI:...
    Downloads: 5 This Week
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  • 4

    DualTranscriptDiscovery

    Transcript-discovery approach for gene feature delimitation by RNA-seq

    This project contains Python scripts usable for a dual transcript-discovery approach that improves the delimitation of gene features from RNA-seq data in the chicken model. Documentation: http://bio.biologists.org/content/biolopen/suppl/2018/01/17/bio.028498.DC1/BIO028498supp.pdf Citation: Orgeur M., Martens M., Börno S. T., Timmermann B., Duprez D. and Stricker S. (2018). A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken...
    Downloads: 0 This Week
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  • 5
    ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML).
    Downloads: 0 This Week
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  • 6

    MethyMer

    Design of specific primer combinations for bisulfite sequencing

    MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc. MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). It also incorporates TCGA CpG methylation...
    Downloads: 1 This Week
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  • 7
    nmr-nessy

    nmr-nessy

    NMR relaxation dispersion spectroscopy analysis software

    NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models.
    Downloads: 0 This Week
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  • 8
    mitoMaker

    mitoMaker

    mitoMaker - a mitochondria assembly and annotation script

    ... a target mitochondrial genome given. 2-searches for all mitochondrial gene features and circularization. 3-stores the best result found. 4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps. 5-annotates the best assembly, identifying the start and end position of each and every feature. 6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile).
    Downloads: 0 This Week
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  • 9
    diCal-IBD

    diCal-IBD

    diCal-IBD predicts identical by descent tracts using sequence data

    diCal-IBD can be used for predicting identical by descent (IBD) tracts in sequence data. It provides means for calculating the accuracy of the prediction, if the true tracts are available, plotting of the predicted tracts, their TMRCA (time to the most recent common ancestor) and corresponding posterior probabilities, and identification of putative recent positive selection through investigation of average IBD sharing
    Downloads: 0 This Week
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  • 10

    mitoMaker

    mitoMaker - a mitochondria pipeline wrapper script

    Mitomaker is a pipeline wrapper, result analyzer and automated annotator, written in Python v2.7, that, with the help of other programs, builds, analyzes, looks for the best build and annotates target genomes (such as mitochondria and cloroplast). It could be used with other targets, such as specific genes, or transcriptomes, even though that is not it's primary goal, nor thoroughly tested. After various attempts to build different mitochondrial genomes in the lab I studied, a general...
    Downloads: 0 This Week
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  • 11
    Java Machine Learning Library is a library of machine learning algorithms and related datasets. Machine learning techniques include: clustering, classification, feature selection, regression, data pre-processing, ensemble learning, voting, ...
    Downloads: 2 This Week
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  • 12
    SeqSelector

    SeqSelector

    Tools to select sequences for capture enrichment of next-gen libraries

    The SeqSelector toolset is a suite of user-friendly, platform independent python scripts to facilitate selection of sequences for targeted enrichment of next-generation libraries through hybridization-based sequence capture. The scripts require no knowledge of programming, and can be applied to genome sequences of model or non-model species. We suggest a workflow in which genes of interest are first identified from previous studies and publicly available datasets of functional gene annotation...
    Downloads: 0 This Week
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  • 13
    ScreenSifter

    ScreenSifter

    ScreenSifter is a unique tool for RNAi Screen analysis and management

    ScreenSifter can help you in managing all your RNAi screens related projects in organized fashion. ScreenSifter, to perform the sequential, user friendly, guided, and advanced statistical analyses of RNAi screening results. User can upload their raw signal intensities and will avail complete quality control of screen, hit selection, plotting of hit genes with gene ontology, comparing of replicates or comparing of channels. In addition, ScreenSifter has visualization tools to plot specific genes...
    Downloads: 0 This Week
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  • 14

    CDSbank

    multi-sequence extraction, filtering & formatting

    CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5’ and 3’ ends, full taxonomic data, and a heuristic to rank the scientific interest of a species. This rich information allows fully automated data set preparation with a level of sophistication that meets or exceeds manual processing. Defaults ensure ease of use for typical...
    Downloads: 0 This Week
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  • 15

    lonestar

    A feature selection and classification algorithm based on L1 Norm SVM

    A feature selection and classification algorithm. It is based on L1 Norm Support Vector Machine with t-test and Recursive Feature Elimination.
    Downloads: 0 This Week
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  • 16
    GEPETTO - Gene Prioritization in Java

    GEPETTO - Gene Prioritization in Java

    GEPETTO (GEne Prioritization ExTended TOol)

    GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein...
    Downloads: 0 This Week
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  • 17

    SpiKeDeteKt

    An automatic spike detection program to be used with new KlustaKwik

    This is an automatic spike detection program which takes account of probe geometry and produces a .mask file to be used with the new masked version of KlustaKwik. We recommend you use Python 2.6 or 2.7, e.g. a free academic version can be obtained from Entthought Python. The input files for SpiKeDeteKt are: .dat (raw data file) .probe (probe file, described below - user constructed) parameters.py (optional - otherwise it uses defaultparameters.py) SpiKeDeteKt outputs...
    Downloads: 0 This Week
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  • 18
    imDEV

    imDEV

    Tools for multivariate data visualization, exploration and analysis.

    You may also like some newer work: http://createdatasol.com/ Project imDEV is an application of RExcel, which seamlessly integrates Excel and R for tasks focused on multivariate data visualization, exploration, and analysis. Interactive modules for dimensional reduction (imPCA), prediction (imPLS), feature selection, analysis of correlation (imCorrelations) and generation of networked structures (imGraph) provide an integrated environment for systems level analysis of multivariate data.
    Downloads: 1 This Week
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  • 19
    Protein ALignment Optimizer
    Protein ALignment Optimiser (PALO) is a script for the selection and alignment of the best combination of transcripts among orthologous genes. PALO is mainly written in Python, although other programming languages are also implemented (R, Perl...).
    Downloads: 0 This Week
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  • 20
    Java GUI to analyze one (or more, in batch mode) datasets with several feature selection methods at the same time and also performing an "ensemble" analysis. It can be easily extended to include any feature selection algorithm.
    Downloads: 0 This Week
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  • 21
    DimReduction project provide an open-source multiplatform (Java) graphical environment for bioinformatics problems that supports many feature selection algorithms, pattern recognition techniques, criterion functions and graphic visualization tools.
    Downloads: 0 This Week
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  • 22
    A collection of tools for use in gene naming, including standardization, selection, and comparison.
    Downloads: 0 This Week
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  • 23
    A small simulator for Mendelian genetics, genetic drift, natural selection and random mutations, built on matplotlib and wxpython. A graph will be generated that traces the distribution of genotypes at successive generations.
    Downloads: 0 This Week
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  • 24
    Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
    Downloads: 0 This Week
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  • 25
    A python library for handling and analyzing biological sequence annotations as described in GFF files (General Feature Format). The library is intended to be a complete framework for this file format.
    Downloads: 0 This Week
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