Search Results for "package"
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Showing 40 open source projects for "package"
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1
Astropy
Repository for the Astropy core package
...The Anaconda Python Distribution includes Astropy and is the recommended way to install both Python and the Astropy package. The astropy package contains key functionality and common tools needed for performing astronomy and astrophysics with Python. It is at the core of the Astropy Project, which aims to enable the community to develop a robust ecosystem of affiliated packages covering a broad range of needs for astronomical research, data processing, and data analysis. -
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clusterProfiler
A universal enrichment tool for interpreting omics data
clusterProfiler is an R/Bioconductor package that provides a unified workflow for functional enrichment analysis to interpret high-throughput omics results. It supports both over-representation analysis and gene set enrichment analysis, letting you work with unranked gene lists or ranked statistics from differential pipelines. The package connects to multiple knowledge bases—such as Gene Ontology, KEGG, Reactome, Disease Ontology, MeSH and others—through a consistent interface so you can query different biological lenses without rewriting code. ... -
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awesome-single-cell
Community-curated list of software packages and data resources
...Rapid, accurate and memory-frugal preprocessing of single-cell and single-nucleus RNA-seq data. Find bimodal, unimodal, and multimodal features in your data. Ascend is an R package comprised of fast, streamlined analysis functions optimized to address the statistical challenges of single cell RNA-seq. The package incorporates novel and established methods to provide a flexible framework to perform filtering, quality control, normalization, dimension reduction, clustering, differential expression and a wide-range of plotting. ... -
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hctsa
Highly comparative time-series analysis
hctsa is a Matlab software package for running highly comparative time-series analysis. It extracts thousands of time-series features from a collection of univariate time series and includes a range of tools for visualizing and analyzing the resulting time-series feature matrix. -
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Cookiecutter Data Science
Project structure for doing and sharing data science work
A logical, reasonably standardized, but flexible project structure for doing and sharing data science work. When we think about data analysis, we often think just about the resulting reports, insights, or visualizations. While these end products are generally the main event, it's easy to focus on making the products look nice and ignore the quality of the code that generates them. Because these end products are created programmatically, code quality is still important! And we're not talking... -
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xrayutilities
a package with useful scripts for X-ray diffraction physicists
xrayutilities is a python package used to analyze x-ray diffraction data. It can support with performing diffraction experiments and used for common steps in the data analysis. It can read experimental data from several data formats (spec, edf, xrdml, ...); convert them to reciprocal space for arbitrary goniometer geometries and different detector systems (point, linear as well as area detectors); for further processing the data can be gridded (transformed to a regular grid). ... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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Hyperspectral data analysis in R
Handling and basic analysis of hyperspectral data in R
The hsdar package contains classes and functions to manage, analyse and simulate hyperspectral data. These might be either spectrometer measurements or hyperspectral images through the interface of rgdal. -
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Parallel and Distributed Process System
OmniSim simulates parallel and distributed processing systems
Parallel and Distributed Process OmniSim Computational Neuroscience: Large-scale neural population dynamics, brain-inspired computing architectures, and neuro-symbolic AI systems 🧬 Scientific Overview PDP-OmniSim is an advanced computational framework for simulating parallel and distributed processing systems, with cutting-edge applications in computational neuroscience, distributed computing, and complex systems modeling. The framework provides researchers with robust tools for... -
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Python Laboratory Operations Toolkit
many useful snippets for using python in a laboratory
...Includes support for such protocols as VXI-11 (and its extension, LXI), Vernier LabPro (now very old), and National Instruments DSTP (now very old). Also includes data analysis and modelling tidbits. Python3 updates are on the way in the very near future for the biggest packages. the vxi11 package is fully up-to-date, although see the blog post about python 3.13 -
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Log4jScanner
A log4j vulnerability filesystem scanner and Go package
log4jscanner is a filesystem scanner and Go package that helps organizations quickly identify vulnerable Log4j components inside JARs and shaded dependencies. Instead of probing networks, it walks directories and archives, including nested JARs, to find version fingerprints and risky classes associated with the Log4Shell family of issues. The focus on static analysis makes it suitable for container images, build artifacts, and offline systems where active scanning isn’t feasible. ... -
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BDS
Blockchain data parsing and persisting results
JD Cloud Blockchain Data Service (BDS) is a real-time data aggregating, analyzing, and visualization service for chain-like unstructured data from all kinds of 3rd party Blockchains. Splitter is the key module of Blockchain Data Service (BDS) and provides data analysis capability. Splitter is responsible for consuming blockchain data from message queue (kafka) and inserting data into persistent data storage services (relational database, data warehouse, etc.) for further processing. Before... -
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TONIC
Analysis of neural spiking data generated by multi-electrode arrays
A neuroscience data analysis package for handling extracellular potentials recorded by multi-electrode arrays, including signal processing, event detection, feature extraction, and spike sorting. -
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Short-3DXRD
Data analysis package for 3D-XRD
Please contact the authors by sending a message (via https://sourceforge.net/users/rmhuizenga). We will be glad to send you the programs. -
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SPRITE
Parallel SNP detection pipeline
SPRITE is an open-source software package providing a parallel implementation of the Single Nucleotide Polymorphisms (SNP) detection genomic data analysis workflow. It consists of three tools: PRUNE for read alignment, SAMPA for intermediate file processing, and PARSNIP for parallel SNP calling. -
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Pyclamp
A Python package used to extract and analyse electrophysiological data
...Quantal analysis : This part of the package performs simple variance-mean analysis and Bayesian quantal analysis to estimate the quantal sizea dn number of release sites among other measures. -
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ExAM-Exome_Analysis_And_Mining
A whole exome sequencing analysis package and its graphical interface
...However, these data remain difficult to analyze and interpret by the general scientific community, due to the limited bioinformatics resources that are currently freely available for their analysis and the partial information that they provide. Here, we present an interactive and free analysis package, ExAM, dedicated to whole exome sequencing data analysis. It is accessible to non-computer scientists and provides a complete set of information, as well as decision support to prioritize candidate disease causing variants. -
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Seer
Seer is a multipurpose data analysis package for Monte Carlo data.
Seer is a multipurpose data analysis package for Monte Carlo simulation data, particularly for collider physics processes. Seer reads LHCO files and performs a variety of cuts and analyses on the data for either exploratory data analysis or reproduction of experimental studies. -
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A collection of code, bundled into a single R package, to perform several aspects of data management, image pre-processing, data analysis and statistical inference related to the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI).
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ThermV
Comprehensive thermal analysis software package
ThermV thermal analysis software package aims to provide the most sophisticated automatic analysis of thermal analysis data (TG/DTG, DTA and DSC). It offers new algorithm for concurrent peak deconvolution at different heating rates and provides full kinetic analysis of these data, including isoconversional methods for Ea, determination of reaction model and full kinetic triplet, Avrami coefficients, and dimensionality of crystal growth for reactions in the solid state. -
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Grid3D Toolbox
3D grid toolbox for analysis of molecular simulations
"Grid3D Toolbox" is a set of command line tools for visualization and analysis of the results of molecular simulations based on 3-dimensional density maps (grids). Currently, the tools only work with the simulation trajectories generated by the GROMACS simulation package (http://www.gromacs.org/). The generated density maps are saved in the Grid3D native .g3d format and can be visualized using a third party data visualization software. A converter from the .g3d format to .vti, an XML based format of the VTK library is provided with the "Grid3D Toolbox", so that the generated density maps can be visualized using the ParaView data analysis and visualization software (http://www.paraview.org). ... -
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BriPy
A BRIC-seq data analysis package written in Python.
...It employs metabolic labeling by BrU of newly synthesized RNAs to chase chronological decreases of BrU-labeled RNA (Pulse-chase labeling), followed by immunoprecipitation with antibody for BrU, construction of cRNA library for High-throughput sequencing and computational data analysis. -What is BriPy? BriPy package is a BRIC-seq data analysis tool written in Python. It can calculate RNA half-life for each transcript and draw graphs describing the kinetics of RNA decay. In the future, it will provide several useful modules(e.g. calculating RPKM of each transcript from BAM file or ELAND output file). -Prerequisites To use BriPy package, you will need Python and the following extension packages. ... -
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EnvStats
An R Package for Environmental Statistics
EnvStats is an R package for environmental statistics. It is the open-source successor to the commercial module for S-Plus© called "EnvironmentalStats for S-Plus", which was first released in April, 1997. The EnvStats package, along with the R software environment, provides comprehensive and powerful software for environmental data analysis. EnvStats brings the major environmental statistical methods found in the literature and regulatory guidance documents into one statistical package, along with an extensive hypertext help system that explains what these methods do, how to use these methods, and where to find them in the environmental statistics literature. ... -
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vonMises
Package for dealing with the von Mises periodogram
This is the package of C++ programs facilitating the practical use of the von Mises periodogram. The von Mises periodogram is a data-analysis period-search tool that models the periodic signal with the so-called von Mises function, K exp(nu cos x). The package can be used to compute the periodogram itself, as well as its detection significance levels.
