Search Results for "r package xmsannotator" - Page 5
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Showing 196 open source projects for "r package xmsannotator"
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DiffCorr
an R package to analyze differential correlations biological networks
DiffCorr can explore differential correlations between different conditions in a modern post-genomics data including transcriptomics and metabolomics. DiffCorr package might prove useful for identifying various differential correlations and for detecting biomarker candidates. -
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We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. License: The DSS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely...
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EXCAVATOR2tool
Enhanced tool for detecting CNVs from whole-exome sequencing data
ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!! We recently published on BMC Genomics a novel software package, named XCAVATOR, for the identification of CNVs/CNAs from short and long reads whole-genome sequencing experiments (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/. EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing... -
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SWire4R
An R package enabling R to interact with Stata for data exchange
Swire4R is an R package for exchanging data between R and Stata. SWire4R uses SWire for connecting R to Stata. SWire is a plugin for Stata >=13 which acts like a server: client applications can query SWire for interacting with Stata. SWire4R acts like a client application for Swire, providing the user with various basic functions for retrieving data from Stata and exporting data to Stata. SWire4R must be compiled by R. For more information about SWire, visit https://sourceforge.net/projects... -
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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax... -
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An open-source implementation of our network-based target deconvolution approach, named target addiction score (TAS). License: The TAS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY...
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Quake Shareware HD (High Definition)
Quake in High Definition
Quake in High Definition for DVD-ROM discs. Old YouTube video at: http://www.youtube.com/watch?v=qL2pJwINjSM -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple... -
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iHeatmap
Build a heatmap through interactive way
Help researcher to build a heatmap through interactive way. Now use python to provide a GUI for a public R package heatmap3. Users need to install heatmap3 package from CRAN. -
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Strandseq-InvertR
predicts inversions in Strand-seq data
Invert.R is a custom, R-based bioinformatic package that localizes and genotypes putative inversions in single cells. The program systematically assesses strand orientation of Strand-seq libraries using a read-based sliding window strategy to calculate Watson-Crick ratios. It assigns locale strand states based on these ratios and predicts inversions based on regional changes in strand state. The source code of this package is freely available. -
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CanReg5 (moved to Github)
Canreg5 is a software package for population based cancer registries
Cancer registries need a tool to input, store, check and analyse their data. If these data are also coded and verified in a standard way, it facilitates the production of comparable analyses across registry populations. The main goal of the CanReg5 project is to provide a flexible and easy to use tool to accomplish these objectives. CanReg5 is a multi user, multi platform, open source tool to input, store, check and analyse cancer registry data. It has modules to do: data entry,... -
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hSDM
R package for hierarchical species distribution models
hSDM is an R package for hierarchical species distribution models. Such models allows interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting... -
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This is an R package for the Mass spectrometry Research. The MrR can be used to analyze the mass spectrometry data for baseline correction, denoising, peak detection, peak alignment, peak normalization, and biomarker discovery.
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EDDA
Experiment Design for Differential Abundance Analysis
.... “The Importance of Study Design for Detecting Differentially Abundant Features in High-Throughput Experiments.” Genome Biology 2014;15(12):527 (http://www.ncbi.nlm.nih.gov/pubmed/25517037/). An accompanying web server (http://edda.gis.a-star.edu.sg/) is available for easy access to some functionality of EDDA. Additionally a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/EDDA.html) is available for easy installation of EDDA R package. -
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miRLAB
miRLAB: an R package for exploring miRNA-mRNA regulatory relationships
miRLAB is an R package for automating the procedure of inferring and validating miRNA-mRNA regulatory relationships. The package provides a complete set of pipelines for testing new methods and analysing new expression datasets. miRLAB includes a pipeline to obtain matched miRNA and mRNA expression datasets directly from The Cancer Genome Atlas (TCGA, based on TCGA Assembler), the benchmark computational methods for inferring miRNA-mRNA regulatory relationships, the functions for validating... -
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FuncEpiMod
Identification of Functional Epigenetic Modules (FEM)
An R-package implementing an algorithm, called FEM, for identifying genes modules of coordinated differential expression and differential methylation associated with a phenotype of interest. The modules are inferred as heavy subgraphs on an interaction network where weights are constructed from the statistics of differential expression and differential methylation. Note: latest version of R-package will be available from Bioconductor (www.bioconductor.org) -
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This site contains four packages of Mass and mass-based density estimation. 1. The first package is about the basic mass estimation (including one-dimensional mass estimation and Half-Space Tree based multi-dimensional mass estimation). This packages contains the necessary codes to run on MATLAB. 2. The second package includes source and object files of DEMass-DBSCAN to be used with the WEKA system. 3. The third package DEMassBayes includes the source and object files of a Bayesian...
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LowMACA
Low frequency Mutation Analysis via Consensus Alignment
The remarkable efforts recently carried out to fully understand the mutational landscape of various kinds of cancer have revealed that the mutational processes can be extremely variable depending on the tumor type and the clinical features of patients. Thanks to these efforts, we have reached a clear picture of the most commonly mutated genes in various types of cancer. However, we are still far from a complete picture of rarely mutated genes, which can be an important target for... -
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CoGA
R package for differential co-expression analysis
CoGA (Co-expression Graph Analyzer) is an R package to identify differentially co-expressed gene sets between two phenotypes. The software infers gene regulatory networks from gene expression data, and compares structural properties of the inferred networks based on their spectrum distributions. It also compares the networks in terms of their gene centralities, clustering coefficients and shortest path lengths. In addition to the differential co-expression analyses, the tool provides graphical... -
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NetView P
Population Genomics Network Analysis Pipeline
NetView P has been re-structured as a package for R and moved to GitHub: https://github.com/esteinig/netview -
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Drug Extraction
Drug name extraction
Drug name recognition and normalisation/grounding to DrugBank ids and standard names. Package provides 2 taggers: 1. DrugTagger - CRF-based with DrugBank presence feature (see feature set for details). 2. DrugnameGazetteer - gazetteer/dictionary-based. Dictionary created from DrugBank.ca database. Both taggers include grounding/normalisation to DrugBank ids and standard names. Feature set: Word, Word-1, Word+1, Word-1_Word, Word_Word+1, DrugBankPresence, POS DrugBankPresence feature... -
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Tux Hat Linux
What you see, is what you get! GNU/Linux Arch Based Distro
.../unixwz0r # Info: The Live ISO is under 700mb and can be put on a CD-R/DVD-R/USB and boot up on any x86 & x86_64 PC computers. Fluxbox has a simular config to FluxBSD, and Fluxbox has been updated to 1.3.7. # IRC Freenode: irc.freenode.net #bsdgeekclub @UNIXwz0r (owner) Tux Hat Linux Project # More Screenshots http://ipodpunker.deviantart.com -
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Hackathon for Outbreak Analysis in R
A hackathon for the analysis of disease outbreaks in R
This is the sourceforge project supporting "Hackout: A hackathon for the analysis of disease outbreaks in R". It includes a repository for the collective development of the project's R package. -
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EsiAisParser
Robust Automatic Identification System Parser in Java
This package supports the parsing of AIS messages in Java. AIS, the Automatic Identification System, is a system aiming at improving maritime safety by exchanging messages between ships, other vehicles in particular aircraft involved in search-and-rescue (SAR), and (fixed) base stations. To be precise, this package support the ITU-R M.1371-4 AIS standard. See our extensive javadoc and in particular the class AISParser for more information on how to use this package. See the ESI AIS Parser... -
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DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
... in discerning differential gene expression across diverse conditions. Computational biology is in need of methods for integration of static networks and gene expression data, since it provides interesting insights into the dynamics of biological systems. DEN is an R/Bioconductor based package designed to assemble different types of human bio-molecular interactions as a complete interactome and contains functions to extract dynamic active networks by integration of gene expression data.