Search Results for "python data analysis"
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Showing 143 open source projects for "python data analysis"
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Stanford Data Miner
Tools for integration and analysis of heterogeneous immunological data
An extensive description of this system is published in the Journal of Translational Medicine (http://www.translational-medicine.com/). In brief, the system consists of two main web applications, a data integration app and a data exploration app. The data integration app is a fully custom Java "Web 2.0" product called Sherpa. Sherpa uses Seam, a platform integrating Asynchronous JavaScript and XML (AJAX), JavaServer Faces (JSF), the Java Persistence API (JPA), and Enterprise Java Beans... -
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BioSig is a software library for processing of biomedical signals (EEG, ECG, etc.) with Matlab, Octave, C/C++ and Python. About 50 different data formats are supported.
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R packages (maintained by YJLEE)
R packages for PK/PD modeling , BE/BA, drug stability, ivivc, etc.
These R packages are developed for data analysis of PK/PD modeling & simulation, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM). -
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Grassroots DICOM
Cross-platform DICOM implementation
Grassroots DiCoM is a C++ library for DICOM medical files. It is accessible from Python, C#, Java and PHP. It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE and deflated transfer syntax. It comes with a super fast scanner implementation to quickly scan hundreds of DICOM files. It supports SCU network operations (C-ECHO, C-FIND, C-STORE, C-MOVE). PS 3.3 & 3.6 are distributed as XML files. It also provides PS 3.15 certificates and password based mecanism to anonymize and de-identify DICOM datasets. -
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SDF Merger
Desktop application for merging multiple SDF files into a single SDF
SDF Merger is a Python-based desktop application designed for chemists and researchers working with molecular data. The tool provides an graphical interface to merge multiple SDF files containing chemical structures and properties into a single consolidated file. Key Features: 1. User-Friendly GUI: Clean, professional interface with corporate branding 2. -
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GrowthRates
Calculate growth rates from microplate reader output
...CGR2 (Compare Growth Rates) is a statistical program specifically designed to assess the results of a growth rate experiment that has been analyzed using the program GrowthRates. The purpose of a statistical analysis is to establish our level of trust in both the data and in the conclusions we draw from that data. Both the GrowthRate and CGR2 packages are -
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SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
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SimPET
A web platform for the MC simulation of realistic brain PET data
SimPET (http://www.sim-pet.org) is an open, efficient, and user‐friendly online platform for the generation of synthetic brain PET datasets. The platform offers the ability to generate realistic activity and attenuation maps from patient's PET/CT and MRI images. These maps can then be simulated, and sinograms and simulated images can be downloaded. More advanced features can be obtained by using the SimPET... -
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Gait Analysis Graphical User Interface
Extracts gait parameters from 120 fps video of mouse walking
...This was developed and used in the laboratory of Veronique VanderHorst, MD PhD at Beth Israel Deaconess/Harvard Medical School. First, a GUI displays videos of mice walking on a custom apparatus and enables the user to manually detect paw position. This data is saved. Additional functions take this spatiotemporal information and extract commonly used gait parameters, which are then exported to a MATLAB structure to be used for scientific analysis. -
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OpenVigil
Open pharmacovigilance data extraction, mining and analysis tool
OpenVigil provides a webinterface to analyse pharmacovigilance data, i.e., spontanous or systematic collections of treatments (drugs) and observed adverse events ("drug side effects"). FDA Adverse Event Reporting System (AERS) and other pharmacovigilance data (e.g., Canadian or German) are supported. The OpenVigil web-based analysis tools offer several analysis modes like extraction, filtering, mining of data and analyses via measurements of disproportionality like proportional reporting ratio or reporting odds ratios) and export to spreadsheets programs like Microsoft Excel or statistics programs like R. ... -
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OmicSelector
Feature selection and deep learning modeling for omic biomarker study
OmicSelector is an environment, Docker-based web application, and R package for biomarker signature selection (feature selection) from high-throughput experiments and others. It was initially developed for miRNA-seq (small RNA, smRNA-seq; hence the name was miRNAselector), RNA-seq and qPCR, but can be applied for every problem where numeric features should be selected to counteract overfitting of the models. Using our tool, you can choose features, like miRNAs, with the most significant... -
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KARDIA ("heart" in Greek) is a Matlab software with a graphic user interface designed for the analysis of cardiac interbeat interval data.
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ECG Logger Viewer
ECG Logger Viewer is the application software for ECG Logger device.
NEW VERSION 3.2.1.5 - MARS 2022 ECG Logger is a Wearable Cardio Monitor for Long-Term (up to 24h) ECG Data Acquisition and Analysis (aka Holter) with an ECG live (real-time) mode. The ECG Logger project is aimed for providing a very low-cost open-source "Hardware and Software" for a Cardiac Rhythmic Holter. The hardware has been made very simple and is based on an Arduino Nano micro-controller with two companion boards for the SD card mass-storage and the instrumentation differential amplifier. ... -
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ECG Logger
ECG Logger is a complete Holter system incl. device and firmware.
NEW V3 version with RTC and buzzer (require V3+ ECG Logger Viewer application) The ECG Logger project is a Wearable Cardio Monitor for Long-Term (up to 24h) ECG Data Acquisition and Analysis (aka Holter) with an ECG live (real-time) mode. This project provides a very low-cost open-source "Hardware and Software" for a Cardiac Rhythmic Holter. The hardware has been made very simple and is based on an Arduino Nano micro-controller with boards for SD card mass-storage, instrumentation differential amplifier and RTC. ... -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support... -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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DDMaker
Local Distribution Density Map Maker
DDMaker perform local density analysis and generates pseudocolor maps of the spatial distribution of imaged cellular structures in 2D images, starting from either RGB color, grey level or binary images. DDMaker local density analysis permit to selectively denoise the signal, visualize and quantify its distribution and threshold the image basing on local density. -
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Peptide Vaccine Analysis Tool (PVAT) is an optimization software that predicts the best possible peptide stretches in a given protein sequence based on two factors: 1. the surface exposure of the peptide stretches, and 2. their susceptibility to mutation.
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medical image analysis
Libraries and command line tools for medical image processing.
This software provides libraries and command line tools for the processing and analysis of gray scale medical images. -
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The Development System for Auditory Modelling (DSAM) is a computational library designed specifically for producing simulations of the auditory system. It brings together many established auditory models within a flexible programming platform.
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DBSolveOptimum
The software for systems biology/pharmacology modeling
DBSolveOptimum is a stand-alone software tool for the construction and analysis of mathematical models of biological systems. It is a succession and extension of DBSolve 5 and DBSolve 7, which were popular tools for systems biology. In addition to the capabilities of these software packages, DBSolveOptimum is implemented with new tools for extended data analysis and multiple simulations, which are important for simulation of virtual clinical trials and application of modern modeling techniques, like quantitative systems pharmacology, to problems arising in drug research and development. ... -
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ICDtools
Tools for ICD (International Classification of Diseases) data
Currently implemented: Python parser to import ICD10 XML data into a relational PostgreSQL database Sponsored by Ordium Biotechnology https://ordium.ai MIT License -
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LymPHOS2
LymPHOS2 Web-App
... - Nguyen, TD., Vidal-Cortes, O., Gallardo, Ó., Abian, J., Carrascal, M., LymPHOS 2.0: an update of a phosphosite database of primary human T cells. Database 2015, 2015. DOI: 10.1093/database/bav115 - Carrascal, M., Ovelleiro, D., Casas, V., Gay, M., Abian, J., Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment. J. Proteome Res. 2008, 7, 5167-5176. DOI: 10.1021/pr800500r - Ovelleiro, D., Carrascal, M., Casas, V., Abian, J., LymPHOS: design of a phosphosite database of primary human T cells. Proteomics 2009, 9, 3741–3751. DOI: 10.1002/pmic.200800701 - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., Abian, J., A collection of open source applications for mass spectrometry data mining. ... -
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TCellXTalk
TCellXTalk Web-App from LP CSIC/UAB
TCellXTalk is a comprehensive database of experimentally detected phosphorylation, ubiquitination and acetylation sites in human T cells. The web-app at www.TCellXTalk.org makes TCellXTalk accessible from Internet, and enables the in silico prediction of potential co-modified peptides to facilitate their experimental detection, using targeted or directed mass spectrometry, for the study of protein post-translational modification cross-talk. More detailed information on TCellXTalk and... -
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Pydicom by examples
Basic and intermediate examples of DICOM library with Jupyter
Basic and intermediate examples to read, modify and write DICOM files with Python code using Jupyter - To install Jupyter - https://jupyter.org/install ====== All examples are based on Pydicom. An open source library - https://pydicom.github.io/
