Search Results for "libbiosig-3.dll"
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Showing 41 open source projects for "libbiosig-3.dll"
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SPiCEv2.1
Splicing Prediction in Consensus Element
...To access the tool's predictions, please use SPiP, accessible at : https://sourceforge.net/projects/splicing-prediction-pipeline/ or https://github.com/raphaelleman/SPiP If you have questions, please contact me to: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr v2.1.5 (05/2019) + corr (01/2020): Fix bug for linux version v2.1.4 (03/2019): Proxy management (only for Windows version) v2.1.3 (07/2018): correction bug for first 3' ss import vcf file v2.1.2 (06/2018): Import duplication Simplify import of deletion with one nucleotide Use tryCatch Improving web api connection check -
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COHCAP
City of Hope CpG Island Analysis Pipeline
...Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download -
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Virtual Laboratory Environment
A multi-modeling and simulation environment to study complex systems
...The models can be developed with the DEVS formalism or with the classical mathematical formalism: Ordinary Differential Equation with Euler, Range-Kutta or QSS integrator, Finite state automaton (FDDEVS, UML State chart, Hybrid Petri net). The VLE environment provides an IDE to develop C++ models, DEVS coupled models. VLE have also three ports to use the VFL with Python, Java and R programming languages. -
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bspipe
An End-to-End Analysis Pipeline for BS-seq
BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files for visualization, and (9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq. -
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fscaret_shiny
UI for fscaret
User Interface (ui) application which implements the automated feature selection provided by the 'fscaret' package of R-environment. -
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Panacea
PAN And Core-gEnome Analysis
A tool to calculate the Pan-Genome of a set of annotated genomes -
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Community Detection Modularity Suite
Suite of community detection algorithms based on Modularity
- MixtureModel_v1r1: overlapping community algorithm [3], which includes novel partition density and fuzzy modularity metrics. - OpenMP versions of algorithms in [1] are available to download. - Main suite containing three community detection algorithms based on the Modularity measure containing: Geodesic and Random Walk edge Betweenness [1] and Spectral Modularity [2]. Collaborator: Theologos Kotsos -
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BayesRate
Bayesian estimation of diversification rates
BayesRate is a program to estimate speciation and extinction rates from dated phylogenies in a Bayesian framework. The methods are described in: Silvestro, D., Schnitzler, J. and Zizka, G. (2011) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11, 311 Silvestro D., Zizka G. & Schulte K. (2014) Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae). Evolution, 68, 163-175. -
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Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity.
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Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
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NOFI ranking
The Non-Outlier Fragment Ion ranking for enhaced DIA quantification
...The outline is as follows: 1) The input contains the list of SWATH fragment ion XICs from the identified and quantified peptides by software tools such as Skyline and OpenSWATH. 2) The first step in NOFI is the computation of the 4 attributes (RTd, FWHMd, IRd and IRrep) used to represent each fragment ion as a vector. 3) Multivariate outlier detection techniques are used to rank all the fragment ions from each peptide. 4) Several figures are generated (a pdf file) to visualize the effect of the Top-N fragment ions over different indicators. 5) The user can choose the number of top fragment ions per peptide, thereby utilizing the optimal subset of high priority Top-N NOFIs for quantification while excluding the impaired fragment ions. -
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The c2001 spatio-temporal mining library
An open source spatio-temporal data mining library
...The General Association Rule Mining Framework(GARMF) library, which support mining association rules from transactions(boolean, weighted, fuzzy), spatial datasets (vector and raster) and spatio-temporal datasets (raster snapshots). Besides it support incremental mining. 2. Rule Filtering Library (RFL), a library for rule evaluation. 3. Besides, DAP-Shell, a GUI shell for GARMF and RFL, will be provided. However I'll pay no more attention on it. -
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TeachingDemos
Bioinformatics related demos and tutorials using the R programming lan
Bioinformatics related demos and tutorials using the R programming language for large biological data. Licence: Creative Commons Attribution-NonCommercial 4.0 International License -
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ADRminer
An R package for the automated generation of drug safety signals
Adverse Drug event Reporting systems miner -
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RIPE (Regulatory network Inference from joint Perturbation and Expression data) is a novel three-step method that integrates both perturbation data and steady state gene expression data in order to estimate a regulatory network. The ripe package is written in R, with additional functionality provided by a MATLAB executable file. The executable file uses a runtime engine called the MATLAB Compiler Runtime (MCR). The executable for different architectures is distributed on this site together with the R package itself.
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SimAssem
For processing and/or simulating species assemblage data.
SimAssem is a tool for investigating the performances of species richness estimators across widely ranging assemblages and survey designs. Assemblages are simulated by specifying the: 1) number of species, 2) total abundance of individuals, 3) abundance distribution, 4) spatial configuration, 5) species detection probabilities, 6) survey design, and 7) number of grid cells to survey (out of a square grid comprised of 10,000 cells). SimAssem also processes existing encounter data and formats existing and simulated encounter data for other programs. SimAssem, along with the open source code, will hopefully give researchers and managers a tool for assessing the development of new estimators and evaluating potential decisions in a simulated environment. ... -
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RawGeno Version 2.0-1 is released! RawGeno is an R CRAN library automating the scoring of AFLP electropherograms. The library includes a graphical user interface to simplify its use. Note that the 2.0-1 version is delivered as a source (*.tar.gz for Linux and Mac users) and as a binary file (*.zip, for Windows users). The installation procedure differs slightly according to your system; but this should remain simple. Have a look at the readme file when you download your new copy...
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SIGGI
Simulation of Ideation Games and Games concerning Ideation
This is the SIGGI program used for a diploma thesis in 2012. It can be used as a solid basis for research concerning Ideation Games (Idea Creation). If you have module requests or want to contribute please contact the author. -
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colonyzer image analysis software
Image analysis estimating cell density in arrayed microbial cultures
Image analysis software for quantification of cell density in microbial cultures (e.g. S. cerevisiae) growing on solid agar plates. Specialises in detection of extremely low cell densities. Forms part of the Quantitative Fitness Analysis (QFA) workflow: http://research.ncl.ac.uk/qfa/ Suitable for high-throughput, genome-wide analysis of culture libraries when combined with the following qfa R package: http://qfa.r-forge.r-project.org/ This is the version presented, used and... -
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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. -
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RMol : SD/Molfile information in R
RMol: Transforming SD/Molfile structure information into R Objects
RMol is an R script with a collection of functions to link information of SD/Molfile structure databases with powerful graph analysis packages in R. -
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...This is a library and a set of applications that can be used to analyze the results of deep sequencing results. (See Li et al.: ANDES: Statistical tools for the ANalyses of DEep Sequencing. BMC Research Notes 2010 3:199.)
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HPCall
Improved base-calling for homopolymer-sensitive next-gen data.
The current software contains the implementation for the 454 pyrosequencing platform.
