Search Results for "cell"
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Showing 814 open source projects for "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 address the statistical challenges of single cell RNA-seq. ... -
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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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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). ... -
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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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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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Themis
Easy to use cryptographic framework for data protection
...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 files to database records. Use Secure Cell to encrypt data at rest. Secure Cell is built around AES-256-GCM, and AES-256-CTR. Secure Message is a simple encrypted messaging solution for the widest scope of applications. Use Secure Message to send encrypted and signed data from one user to another, from client to server, to prevent MITM attacks and avoid single secret leakage. ... -
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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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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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CGAL
The Computational Geometry Algorithms Library
...These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of curves, surface and volume mesh generation, spatial searching, alpha shapes, geometry processing, and many more. The use of these result in beautiful, visually complex and accurate representations. -
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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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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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nichenetr
NicheNet: predict active ligand-target links between interacting cells
...This model of prior information on potential ligand-target links can then be used to infer active ligand-target links between interacting cells. NicheNet prioritizes ligands according to their activity (i.e., how well they predict observed changes in gene expression in the receiver cell) and looks for affected targets with high potential to be regulated by these prioritized ligands. -
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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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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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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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GoNB
GoNB, a Go Notebook Kernel for Jupyter
...As a side benefit it works with packages that use CGO — although it won't parse C code in the cells, so it can't be used as a C kernel. It already includes many goodies: cache between cell of results, contextual help and auto-complete (with gopls), compilation error context (by mousing over), bash command execution, images, html, etc. See the tutorial. It's been heavily used by the author (in developing GoMLX, a machine learning framework for Go), but should still be seen as experimental — if we hear success stories from others, we can change this. -
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JSONLab
JSONLab: compact, portable, robust JSON/binary-JSON encoder
JSONLab is a free and open-source JSON/UBJSON/MessagePack encoder and decoder written in the native MATLAB language. It can be used to convert a MATLAB data structure (array, struct, cell, struct array, cell array, and objects) into JSON/UBJSON/MessagePack formatted strings and files, or to parse a JSON/UBJSON/MessagePack file into MATLAB data structure. JSONLab supports nearly all versions of MATLAB and GNU Octave (a free MATLAB clone). The development of JSONLab is currently funded by the US National Institute of Health (NIH) as part of the NeuroJSON project (data portal https://neurojson.io) under grant U24-NS124027. ... -
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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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Wflow.jl
Hydrological modeling
...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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Dompdf
HTML to PDF converter for PHP
dompdf is an HTML to PDF converter. At its heart, dompdf is (mostly) a CSS 2.1 compliant HTML layout and rendering engine written in PHP. It is a style-driven renderer, it will download and read external stylesheets, inline style tags, and the style attributes of individual HTML elements. It also supports most presentational HTML attributes. PDF rendering is currently provided either by PDFLib or by a bundled version the R&OS CPDF class written by Wayne Munro. (Some important changes have... -
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Memtest86+
Stand-alone memory tester for x86 and x86-64 architecture computers
...The tool can be booted directly via BIOS or UEFI, or through compatible bootloaders, making it highly flexible for troubleshooting unstable systems. It uses advanced testing algorithms specifically designed to detect intermittent, hard-to-find memory errors caused by cell interaction and hardware behavior. With ongoing development and community contributions, Memtest86+ remains a trusted solution for diagnosing memory-related system issues. -
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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.
