Search Results for "cell"
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Showing 76 open source projects for "cell"
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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. -
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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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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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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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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
...You'll always be able to reproduce your collaborators' results. Notebooks are executed in a deterministic order, with no hidden state, delete a cell and marimo deletes its variables while updating affected cells. -
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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,... -
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ipychart
The power of Chart.js with Python
...The charts created are fully configurable, interactive, and modular and are displayed directly in the output of the cells of your jupyter notebook environment. Charts are fully interactive, you can hover it to display tooltips and select the information you want to see directly from the output cell of your notebook. All the types of charts present in Chart.js are exposed in ipychart. Even complex features such as mixed-types charts are available. Charts are highly customizable and all Chart.js options are available in ipychart. You have complete control over the appearance of your chart. -
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Mercury
Convert Python notebook to web app and share with non-technical users
Turn Python notebooks to web applications with open-source Mercury framework. Hide code and add interactive widgets. Non-technical users can tweak widgets and execute notebook with new parameters. The core of Mercury is Open Source under AGPLv3. We provide Mercury Pro with additional features, dedicated support and friendly commercial license. Mercury is a perfect tool to convert Python notebook to interactive web application and share with non-programmers. You define interactive widgets for... -
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papermill
Parameterize, execute, and analyze notebooks
...Instead of manually opening and running a notebook inside JupyterLab or Notebook every time, Papermill lets you inject new values into a specially tagged parameters cell and execute the entire notebook automatically via a script or automation pipeline, which enables robust automation of data analysis, reports, and experiments. This capability is particularly useful in data science and analytics, where a template notebook might be reused for batching reports across dates, customers, or other variables without rewriting code or duplicating notebooks. ... -
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Google Spreadsheets Python
Google Sheets Python API
gspread is a Python API for Google Sheets. A service account is a special type of Google account intended to represent a non-human user that needs to authenticate and be authorized to access data in Google APIs [sic]. Since it’s a separate account, by default it does not have access to any spreadsheet until you share it with this account. Just like any other Google account. To access spreadsheets via Google Sheets API you need to authenticate and authorize your application. Older versions of... -
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nb-clean
Clean Jupyter notebooks of outputs, metadata, and empty cells
nb-clean cleans Jupyter notebooks of cell execution counts, metadata, outputs, and (optionally) empty cells, preparing them for committing to version control. It provides both a Git filter and pre-commit hook to automatically clean notebooks before they're staged, and can also be used with other version control systems, as a command line tool, and as a Python library. It can determine if a notebook is clean or not, which can be used as a check in your continuous integration pipelines. nb-clean can also be used as a pre-commit hook. ... -
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MicroK8s
Single-package Kubernetes for developers, IoT and edge
...A quick install, easy upgrades and great security make it perfect for micro clouds and edge computing. As the publishers of MicroK8s, we deliver the world’s most efficient multi-cloud, multi-arch Kubernetes. Under the cell tower. On the racecar. On satellites or everyday appliances, MicroK8s delivers the full Kubernetes experience on IoT and micro clouds. Fully containerized deployment with compressed over-the-air updates for ultra-reliable operations. MicroK8s will apply security updates automatically by default, defer them if you want. Upgrade to a newer version of Kubernetes with a single command. ... -
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nbcelltests
Cell-by-cell testing for production Jupyter notebooks in JupyterLab
nbcelltests is designed for writing tests for linearly executed notebooks. Its primary use is for unit testing reports. Cell-by-cell testing for production Jupyter notebooks in JupyterLab. To use in JupyterLab, you will also need the lab and server extensions. Typically, these are automatically installed alongside nbcelltests, so you should not need to do anything special to use them. The lab extension will require a rebuild of JupyterLab, which you'll be prompted to do on starting JupyterLab the first time after installing celltests (or you can do it manually with jupyter lab build). ... -
17
KherveSheet
Excel for scientists: high-quality plots, Python in cells, AI side bar
...You have full control over axes, scales, ticks, titles and grids. Curve fitting and peak fitting are supported, with goodness-of-fit reporting overlaid on the plot. Every cell can also run a full Python program, not just a formula. An integrated AI assistant can generate the cell code from a plain-language description if needed. Learn by doing with 300 ready-made scientific examples covering plotting, data analysis, fitting and simulation. Built entirely in Python, KherveSheet adds a familiar Excel-style grid, an optimisation solver, and a native .ksheet format with CSV and Excel import/export. ... -
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The auditory modeling toolbox (AMT) is a Matlab/Octave toolbox for the development and application of auditory computational models. Over 50 auditory models implemented in Matlab, Octave, C, C++, and Python can be run from Matlab and Octave, on Windows and Linux. The AMT provides a well-structured in-code documentation, includes auditory data required to run the models. It integrates functionality to reproduce the model predictions. Model implementations can be evaluated in two stages,...
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TOMUSS
TOMUSS: The Online Multi User Simple Spreadsheet
TOMUSS is an interactive web application (groupware) allowing multiple concurrent users to edit data tables. Its primary goal is the management of students grades. -
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Puzzle Dungeon
A cell-based puzzle game featuring classic and completely new puzzles
Puzzle Dungeon is a free-software game that incorporates classic puzzle games like Sokoban, StoneAge, Atomix, The Minotaur and Theseus, Memory, Fifteen, RotatePic, as well as new puzzles. The game uses pygame and pgzero. It should work well on GNU/Linux, Windows and other Operating Systems. Most levels are generated automatically, offering a new experience every time. Pre-created maps are also supported, including classic collections. Players can reload the same level if stuck -... -
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Pixelization
Stable-diffusion-webui-pixelization
...It's designed as a plugin you install into the Web UI so that in the “Extras” or “Pixelization” tab you can drag in an input image and produce a stylized, block-based version with control over cell size, color depth, and segmentation. The extension uses pre-trained models and optionally can co-operate with the Web UI’s other features (image-to-image, prompt-based generation) so you can combine pixelization with generative workflows. For digital art, game assets, or retro aesthetic workflows, this offers a fast path from photo or high-res asset to stylized tiles or sprites. ... -
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Coq Jupyter
Jupyter kernel for Coq
Make sure that CoqIDE (8.6 or newer) is installed and coqidetop or coqidetop.opt (coqtop for Coq versions before 8.9.0) is in your PATH. Also, make sure the python command is recognized on your machine. If not you can set up an alias for it e.g. python-is-python3 on Ubuntu. There are a number of convenience improvements over standard Jupyter notebook behavior that are implemented to support Coq-specific use cases. -
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databooks
A CLI tool to reduce the friction between data scientists
...Specify paths of notebooks to be checked, an expression or recipe of what you'd like to enforce. databooks will run your checks and raise errors if any notebook does not comply with the desired metadata values. This advanced feature allows users to enforce cell tags, sequential cell execution, maximum number of cells, among many other things. -
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scArches
Reference mapping for single-cell genomics
Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data. scArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations. -
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vim-jukit
Jupyter-Notebook inspired Neovim/Vim Plugin
REPL plugin and Jupyter-Notebook alternative for (Neo)Vim. This plugin is aimed at users in search for a REPL plugin with lots of additional features.
