Search Results for "open cell"
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Showing 380 open source projects for "open cell"
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awesome-single-cell
Community-curated list of software packages and data resources
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. 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... -
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CellTypist
A tool for semi-automatic cell type classification, harmonization
CellTypist is an automated tool for cell type classification, harmonization, and integration. Classification, transfer cell type labels from the reference to query dataset. Harmonization, match and harmonize cell types defined by independent datasets. integration, integrate cell and cell types with supervision from harmonization. CellTypist recapitulates cell type structure and biology of independent datasets. Regularised linear models with Stochastic Gradient Descent provide a fast and... -
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Seurat
R toolkit for single cell genomics
Seurat is a comprehensive R toolkit for single-cell genomics analysis, introduced by the Satija Lab at NYGC. It supports quality control, normalization, clustering, integration of multimodal data (e.g., scRNA‑seq, spatial, CITE‑seq), and visualization. Seurat v5 introduces scalable workflows and spatial transcriptomics support, commonly used in academic and industry research for single-cell studies. -
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Scanpy
Single-cell analysis in Python
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. -
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3DCellForge
AI-powered interactive 3D cell generation and exploration studio
3DCellForge is an AI-powered 3D cell generation and exploration studio built as a polished browser prototype. It uses React, Vite, Three.js, React Three Fiber, Drei, and Framer Motion to create an interactive WebGL environment for exploring biological cell models. Users can rotate, zoom, inspect organelles, compare views, take notes, capture screenshots, and export or import GLB models. The project also supports optional image-to-3D generation through cloud providers and local backends,... -
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harmonypy
Integrate multiple high-dimensional datasets with fuzzy k-means
Harmony is an algorithm for integrating multiple high-dimensional datasets. harmonypy is a port of the harmony R package by Ilya Korsunsky. Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq. -
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pytablewriter
pytablewriter is a Python library to write a table in various formats
pytablewriter is a Python library to write a table in various formats: AsciiDoc / CSV / Elasticsearch / HTML / JavaScript / JSON / LaTeX / LDJSON / LTSV / Markdown / MediaWiki / NumPy / Excel / Pandas / Python / reStructuredText / SQLite / TOML / TSV / YAML. -
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Handcalcs
Python library for converting Python calculations into rendered latex
Handcalcs is a Python library that auto-renders calculation code in Jupyter notebooks or LaTeX documents with step-by-step symbolic substitution, giving output a “handwritten” feel. It supports cell magics and auto-LaTeX generation via configurable output options. -
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Themis
Easy to use cryptographic framework for data protection
Cross-platform high-level cryptographic library. Themis helps to build simple and complex cryptographic features easily, quickly, and securely. It’s a perfect fit for multi-platform apps. Themis hides cryptographic details and eliminates popular mistakes. Themis provides ready-made building blocks (“cryptosystems”) for secure data storage, message exchange, socket connections, and authentication. Secure Cell is a multi-mode cryptographic container suitable for storing anything from encrypted... -
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Flying Carpet
File transfer between Android, iOS, Linux, macOS, and Windows
Send and receive files between Android, iOS, Linux, macOS, and Windows over ad hoc WiFi. No shared network or cell connection required, just two devices with WiFi chips in close range. Don't have a flash drive? Don't have access to a wireless network? Need to move a file larger than 2GB between different filesystems but don't want to set up a network share? Try it out! -
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jQuery Calx
A jQuery plugin for creating formula-based calculation form
jQuery Calx is an Excel calculation engine and formula parser built as a jQuery plugin, it offers spreadsheet ability to process and calculate the formula without bringing a table-like spreadsheet interface. In the core of jQuery Calx is a formula parser generated using jison which parse and processes the formula and set of formulas imported from formula.js. -
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TCG
Terminal cell graphics library
Terminal Cell Graphics (TCG) is a Go library that enables 1-bit graphics rendering in terminal applications using Unicode block symbols. It's designed for developers who want to incorporate simple graphics into CLI tools or games, providing a unique way to display visuals in text-based environments. -
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MBeautifier
MBeautifier is a MATLAB source code formatter, beautifier
MBeautifier is a lightweight M-Script-based MATLAB source code formatter usable directly in the MATLAB Editor. -
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nbmake
Pytest plugin for testing notebooks
Pytest plugin for testing and releasing notebook documentation. To raise the quality of scientific material through better automation. Research/Machine Learning Software Engineers who maintain packages/teaching materials with documentation written in notebooks. -
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nichenetr
NicheNet: predict active ligand-target links between interacting cells
nichenetr: the R implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest. This model of prior information on... -
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Livewire PowerGrid
PowerGrid generates Advanced Datatables using Laravel Livewire
PowerGrid creates modern, powerful and easy-to-customize Datatables based on the Laravel Livewire library. Tables have basic features activated by default. Extend and customize your table including components (checkbox, action buttons, editable fields), global search feature, column data filters, and data export tool. Table components include feature examples. Just uncomment some code, enter your data, and it works. -
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Memtest86+
Stand-alone memory tester for x86 and x86-64 architecture computers
Memtest86+ is a free, open-source, stand-alone memory diagnostic tool designed to thoroughly test system RAM beyond standard BIOS checks. It runs independently of any operating system, allowing it to access nearly all available memory without software or UEFI library limitations. Supporting x86, x86-64, and LoongArch64 architectures, Memtest86+ works on a wide range of modern and legacy hardware platforms. -
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GoNB
GoNB, a Go Notebook Kernel for Jupyter
Go is a compiled language, but with very fast compilation, that allows one to use it in a REPL (Read-Eval-Print-Loop) fashion, by inserting a "Compile" step in the middle of the loop -- so it's a Read-Compile-Run-Print-Loop — while still feeling very interactive. GoNB leverages that compilation speed to implement a full-featured (at least it's getting there) Jupyter notebook kernel. As a side benefit it works with packages that use CGO — although it won't parse C code in the cells, so it... -
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Wflow.jl
Hydrological modeling
...Successfully applied worldwide for analyzing flood hazards, drought, climate change impacts and land use changes, wflow is growing to be a leader in hydrology solutions. Wflow is conceived as a framework, within which multiple distributed model concepts are available, which maximizes the use of open earth observation data, making it the hydrological model of choice for data-scarce environments. Based on gridded topography, soil, land use and climate data, wflow calculates all hydrological fluxes at any given grid cell in the model at a given time step. -
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spyder
The scientific Python development environment
Spyder is a free and open source scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts. It features a unique combination of the advanced editing, analysis, debugging, and profiling functionality of a comprehensive development tool with the data exploration, interactive execution, deep inspection, and beautiful visualization capabilities of a scientific package. Spyder’s multi-language Editor integrates a number of powerful tools... -
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marimo
A reactive notebook for Python
marimo is an open-source reactive notebook for Python, reproducible, git-friendly, executable as a script, and shareable as an app. marimo notebooks are reproducible, extremely interactive, designed for collaboration (git-friendly!), deployable as scripts or apps, and fit for modern Pythonista. Run one cell and marimo reacts by automatically running affected cells, eliminating the error-prone chore of managing the notebook state. marimo's reactive UI elements, like data frame GUIs and plots, make working with data feel refreshingly fast, futuristic, and intuitive. ... -
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tidyr
Tidy Messy Data
tidyr is a core tidyverse package designed to help reshape and clean messy datasets into tidy data—i.e., data frames where each variable is a column, each observation is a row, and each value is a cell. -
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rust_core
A pure Dart implementation of patterns found in Rust's core library
rust_core is a pure Dart implementation of patterns found in Rust's core library, bringing the power of Rust to Dart. -
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node-google-spreadsheet
Google Sheets API wrapper for Javascript / Typescript
node-google-spreadsheet is a JavaScript library that provides a simple interface for reading and writing to Google Sheets, supporting both JavaScript and TypeScript. -
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nbdev
Create delightful software with Jupyter Notebooks
nbdev is a notebook-driven development platform (by fast.ai/AnswerDotAI) enabling you to write code, tests, documentation, and deploy software, all from Jupyter Notebooks. It provides a unified literate programming workflow where you can tag notebook cells for export to Python modules, auto-generate documentation via Quarto (and host it on GitHub Pages), run tests embedded in notebooks, manage clean notebooks with Git-friendly metadata hooks, and seamlessly publish packages to PyPI/conda,...