Search Results for "proxy software tool"
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Showing 15 open source projects for "proxy software tool"
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PANDA
A comprehensive and flexible quantification tool for proteomics data
PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. On the levels... -
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KMWin
Kaplan-Meier for Windows
KMWin (Kaplan-Meier for Windows) is a convenient tool for graphical presentation of results from Kaplan-Meier survival time analysis. The programme is based on the statistical software environment R and provides an easy to use graphical interface. As an introduction, see http://dx.plos.org/10.1371/journal.pone.0038960#s2. -
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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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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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ncPRO-seq
Non-Coding RNA PROfiling from sRNA-seq
ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in... -
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swathTUNER
Software tool for optimizing data-independent acquisition methods
SwathTUNER combines usability and flexibility for the selection of different SWATH data acquisition strategies to address the requirements of multiple experimental conditions. It can be used for any acquisition instrument, including FT-based analyzers, where the same principles with respect to variable precursor isolation windows apply. Fixed and variable windows based on equalizing the distribution of either the precursor ions or the total ion current within each window can be created. -
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PAMGuide
An analysis tool in MATLAB and R for acoustic habitat characterisation
PAMGuide is acoustic analysis software for the characterisation of the acoustic environment from sound recordings. PAMGuide can be used to produce calibrated spectrograms and statistical analyses of sound levels, and is provided in both MATLAB and R. A Tutorial on getting started with PAMGuide can be downloaded here: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12330/suppinfo PAMGuide was published as supplementary material to the following Open Access journal... -
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NGSbinningpytools
Python tools for binning NGS scaffolds to various genomes.
Next generation sequencing has opened new avenues for sequencing prokaryotes which were difficult or either impossible to culture. Now, it is possible to sequence all organisms present in a metagenomic community. However, a critical problem is to determine the host organism for each genomic fragment present in the dataset. This project provides the computational tools for assigning the organismal identity for each genomic scaffold in the given dataset. For more detailed documentation... -
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. ... -
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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... -
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TOPS_CeMM
User Friendly Data Analysis Tool for Interaction Data
TOPS provides the benchtop scientist with a free toolset to analyze, filter and visualize data from functional genomic gene-gene and gene-drug interaction screens with a flexible interface to accommodate various different technologies and analysis algorithms in addition to those already provided here. -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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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... -
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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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A simple tool to help you create an R interface for your Java project. Simply annotate the constructors and methods you want to make available and JAnnotateR will produce a working package, complete with documentation generated from javadocs.
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