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Showing 24 open source projects for "using"
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gogadget
A toolbox for interpretation and visualization of RNA-seq GO analysis
...To install the package download the "gogadget_2.1.tar.gz" file, open R and install with the following line: install.packages( "C:/your/directory/gogadget_2.1.tar.gz", repos = NULL, type="source") The package was made in R 3.4.2 on a Windows 7 computer, and is also tested on Ubuntu. Please cite the following paper if you publish results obtained using gogadget: Nota, B. (2017), Gogadget: an R Package for Interpretation and Visualization of GO Enrichment Results. Mol. Inf. May;36(5-6). doi: 10.1002/minf.201600132. -
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...We have shown its utility in LC-MS/MS and metabolomics in the following two papers: 1) PMID: 19602524. "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition". Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. Bioinformatics 2009 2) "Metabolomics data normalization with EigenMS" Karpievitch YV, Nikolic SB, Wilson R, Sharman JE, Edwards LM. PLoS One 2014
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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. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior. -
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...Please cite: [Khomtchouk et al.: "HeatmapGenerator: High performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." Source Code for Biology and Medicine, 2014 9:30] HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. ...
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Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
...For more details about SuRankCo and its functioning, please see "SuRankCo: Supervised Ranking of Contigs in de novo Assemblies" Mathias Kuhring, Piotr Wojtek Dabrowski, Andreas Nitsche and Bernhard Y. Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet. -
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LiDSiM
LImits of Detection SImulation for Microbes
...For more details about LiDSiM and its functioning, please see "Estimating the Computational Limits of Detection of Microbial Non-Model Organisms" Mathias Kuhring and Bernhard Y. Renard (http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400598/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using LiDSiM. -
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QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).
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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 -
Comet Backup - Fast, Secure Backup Software for MSPsComet is a flexible backup platform, giving you total control over your backup environment and storage destinations.
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BiomeNet
BAYESIAN INFERENCE OF METABOLIC DIVERGENCE AMONG MICROBIAL COMMUNITIES
Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic networks among microbial communities. To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. ... -
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estimate_project
ESTIMATE
ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumors using Expression data) is a new approach to use gene expression signature to infer the fraction of stromal and immune cells in tumor tissues. -
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rTRM
Identification of transcriptional regulatory modules (TRMs)
This R package can be used to identify TRMs using experimental evidence from a single ChIP-seq experiment. It combines computational predicted transcription factor (TF) binding sites, gene expression and protein-protein interaction (PPI) data and use it to predict TRMs. -
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Pop-seq
Population simulator to solve next generation sequencing questions
Pop-seq is a perl based simulation tool, for generating any kind of mapping population using an user defined recombination landscapes. Combined with the Seq-sim tool you can generate pooled or bar-coded next generation sequencing biased outcomes. This tool were used to solve reappearing question in a experimental design (e. g. of how many plants or sequencing depth is advisable in a back crossed or out crossed scenario ) -
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ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
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The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.
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An R package implementation of a consensus clustering methodology. This package allows users to perform re-sampling statistics based clustering using multiple clustering algorithms to assess the robustness of both clusters and members of clusters.
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CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
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Collection of tools for performing robust case-control disease and quantitative trait association studies using Copy Number Variants- Latest version should now be downloaded from Bioconductor
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RmiR is an R package for the analysis of microRNA and gene expression microarrays. The package is designed to coupling microRNA and gene expression data, using different databases, like TargetScan, mirBase, picTar,TarBase and others...
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LD impute
NGS genotype imputation using LD structure
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m0n0merhunter is a command line program for computing the most frequent delta masses of ultra high mass resolution and accurate mass measurements using mass spectrometer data.
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Predictive Networks
Web application providing analysis of biomedical relationships.
Web application providing analysis of biomedical relationships. Built using the Grails web application framework (http://grails.org/) with MySQL (http://www.mysql.com/) as a back-end datastore and utilizing R (http://www.r-project.org/) for statistical analysis. Developed by the Dana Farber Cancer Institute (http://compbio.dfci.harvard.edu/) and Entagen (http://www.entagen.com).
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