Search Results for "python data analysis" - Page 8
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Showing 361 open source projects for "python data analysis"
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NISA
Image Stack Analyzer
OpenCV powered image stack analyser for data extraction and preparation. Can be used in conjunction with nanocalcFX. You can get sample data at the NISA homepage. Currently in pre-alpha state. -
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Genetic data converter
Convert genetic data for hapmixmap software
Genetic data converter, for hapmap.org and hapmixmap data formats. Reads data in tabular format and writes in hapmixmap format. It's possible to add extensions to output different data formats. -
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MaryGold
Variation analysis of metagenomic samples
The package enables detection of sequence variation between metagenomic samples. -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are... -
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SecStAnT
Secondary Structure Analysis Tool for data selection and statistics
SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only... -
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The Complete Genomics Analysis Tools is an open source project to provide tools to simplify analysis of genomics data produced by Complete Genomics.
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GenomeRunner
Annotation and enrichment of Next-Gen sequencing data
...Annotation analysis output - detailed annotation of each genomic region in input data. Used to prioritize individual genomic regions by the total number of epigenomic features they co-localize with. Enrichment analysis output - p-values of statistically significant co-localizations of input genome-wide data with genome annotation features selected for the analysis. -
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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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Systems Glycobiology
Glycosylation Network Analysis Toolbox (GNAT)
...The second version of this software (GNATv2beta.zip) upgrades the original GNAT program with additional features that are geared towards incorporating glycan-structure experimental data into the simulation environment. For information about GNAT installation and usage, please see the GettingStarted.pdf file enclosed in the package. To cite GNAT: [1] Gang Liu, Apurv Puri and Sriram Neelamegham, Glycosylation Network Analysis Toolbox (GNAT): a MATLAB based environment for systems glycobiology, Bioinformatics 2013 29: 404-406 -
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DeDAY
MLE survival analysis: Gompertz, Weibull, Logistic and mixed morality.
DeDAY (Demography Data Analyses) is a tool of analyzing demography data. It supports Gompertz, Weibull and Logistic distributions. DeDay also supports mixed mortality models based on these distribution such as the Gompertz-Makeham distribution. Distributions such as Gompertz describes only age-dependent mortality, which increases over time. Mixed mortality models, such as in Gompertz-Makeham distribution, consider a more general case where mortality is consist of both age-dependent and... -
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BioDare
BioDare is Biological Data Repository focused on timeseries data
BioDare (Biological Data Repository) was developed under the multi-site ROBuST project (http://hallidaylab.bio.ed.ac.uk/ROBuST.html) to support data exchange inside the project. It is a web application which allows data-sharing (including public dissemination), data-processing and analysis, with the main focus on time-series data produced in circadian experiments. -
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TFAST
Software for analysis of afSELEX-seq data
Transcription Factor Analysis using SELEX with High-Throughput Sequencing (TFAST) is software developed by the Mobley lab at the University of Michigan designed to assist with transcription factor binding site discovery using data generated from aptamer-free SELEX-seq (afSELEX-seq). -
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VariabilityAnalysisInNetworks
An R package for identifying biologically perturbed networks
The VAN package enables an integrative analysis of (i) gene expression data with protein-protein interaction networks or (ii) gene and microRNA expression data with microRNA-gene interaction networks to identify biologically perturbed networks. -
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noise-free-cnv
program for analyzing and manipulating DNA microarray data
CNV calling software may produce false-positive calls due to imperfect source material. Direct inspection of the microarray data with the noise-free-cnv software helps to appreciate the quality of the data and to identify artificial calls. With noise-free-cnv it is possible to visualize individual datasets, to compare different datasets and to perform simple transformations. The visualization and the suppression of genomic waves, the comparison of two datasets by subtraction and the... -
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This is the prototype version of software for robust detecting and segmentation of cell nuclei in 3D fluorescence labeled microscopy images. First release coming soon...
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Webapp
A web interface to the SnowyOwl gene prediction pipeline
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RCFPD
Random Collection of Functions for Proteomics Data Analysis
An R package for distribution of data analysis functionality used by the Proteomics Core at Weill Cornell Medical College in Qatar. -
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SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape adds Short linear motif discovery tools to Cytoscape, transforming it into a SLiM discovery platform. A tutorial is available at the following URL: http://bioware.ucd.ie/slimscape/ -
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Onco-STS
A web-based Laboratory Information Management System
Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments. ... -
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PIVOT
PIVOT is a simple yet flexible visualization data tool
PIVOT is a simple yet flexible visualization tool based on Circos (Krzywinski et al., 2009), which offers a fast and aesthetical visualization of data and information. The Protein Interaction Visualization and Observation Tool (PIVOT) was developed specifically for the visualization of protein interaction. It is difficult to spot the proteins that have an interaction when given a large list of proteins but with PIVOT, it is easy to identify the them at a glance. PIVOT displays an image... -
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flNeuronTool
A Fast Light Neuron Tracing and Editor Tool
The flNeuronTool allows users to reconstruct and proofread neuronal morphologies in light microscopy images. The system incorporates automatic tracing and manual editing of neuron reconstruction into a cooperative 3D interactive visualization-assisted environment, which is a powerful tool for analysis of complex neuronal images. -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
...If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism. For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. ... -
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ARDEN
Specificity Control for Read Alignments Using an Artificial Reference
We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation. -
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GenOO-HTS
A Modern Perl Framework for High Throughput Sequencing analysis
GenOO-HTS [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead and complexity of managing the data and the biological entities at hand. ... -
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BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.
