Search Results for "cell negative analysis"
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Showing 103 open source projects for "cell negative analysis"
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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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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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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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toxic-repos
We are against discrediting open source software
toxic-repos is a tool that analyzes GitHub repositories to detect signs of hostile or problematic behavior in open-source communities. It helps developers and contributors identify repositories with negative engagement patterns. -
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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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.NET Interactive
.NET Interactive takes .NET and embeds it into your experiences
.NET Interactive takes the power of .NET and embeds it into your interactive experiences. Share code, explore data, write, and learn across your apps in ways you couldn't before. We recently introduced the .NET Interactive Notebooks extension for Visual Studio Code, which adds support for .NET Interactive using the new Visual Studio Code native notebook feature. We encourage you to try it out. .NET Interactive enables users to mix languages in a single notebook or cell without a wrapper. The... -
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ImportExcel
PowerShell module to import/export Excel spreadsheets, without Excel
ImportExcel is a popular PowerShell module that enables reading, writing, and manipulating Excel spreadsheets without requiring Microsoft Excel to be installed on the host. It exposes straightforward cmdlets like Import-Excel and Export-Excel that convert between Excel sheets and PowerShell objects, making it simple to pipeline tabular data into reporting and automation flows. Advanced features include adding and formatting tables, setting number/date formats, creating charts, and applying... -
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AnaSP
AnaSP, a MATLAB software suite to ANAlyse SPheroids' features
Today, more and more biological laboratories use 3D cell cultures and tissues growth in vitro as model of in vivo tumours and metastasis. However, a lack of methods for quantitative analysis, limits the usage of spheroids as model for routine experiments. AnaSP is a suite tool for automatic analysis of morphological parameters of spheroids starting by brightfield images manually acquired with a standard widefield microscope. -
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Nest-o-Patch
Software for analysis of patch-clamp recordings and other wave data
This program was designed mainly for preconditioning and analysis of electrophysiological data, including patch-clamp and 2-electrode voltage clamp recordings. The program includes tools both for basic analysis of whole-cell recordings or analysis of single channel properties. Program can display and analyse long traces incuding many sweeps, series and even groups simultaneously. Current amplitudes or time intervals are easily measured. -
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TopoIndices
Calculator of topological indices of molecular graphs (from SDF file)
...Anyone can transpile the code to the BBC Basic and execute it on a suitable platform. As I mentioned above - the program "molecules02.bas" is the first step on the way to develop interesting solutions for molecular graph analysis -
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atomes
Analysis, visualization, edition of 3D atomistic models
atomes is a Free (Open Source) cross-platform software licensed under the terms of the Affero GPL v3+ license. atomes is a toolbox developed to analyze, to visualize and to create/edit three-dimensional atomistic models. atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: - Classical MD : DL-POLY and LAMMPS - ab-initio MD : CPMD and CP2K - QM-MM MD : CPMD and CP2K atomes is developed by Dr. Sébastien Le... -
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M32/X32 Show Manager
Reorganize M32/X32 show files
Both the Midas M32 and Behringer X32 share the same design of show management using the console GUI, M32-Edit and X32-Edit apps. This app provides an alternative method to manage these show files (cues, scenes and snippets). It provides an easier method of reorganizing and importing/exporting of files. -
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OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect analysis function and beautiful operation interface of HiPlot (https://hiplot.cn), which I developed based VUE.js and Node.js, etc. -
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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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MLPACK is a C++ machine learning library with emphasis on scalability, speed, and ease-of-use. Its aim is to make machine learning possible for novice users by means of a simple, consistent API, while simultaneously exploiting C++ language features to provide maximum performance and flexibility for expert users. * More info + downloads: https://mlpack.org * Git repo: https://github.com/mlpack/mlpack
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Multicell Thin Walled Beam Analysis
Umut YILMAZ Multi-cell Thin Walled Beam Section Analysis
Finding a shear center is a difficult and time consuming job for multi-cell thin walled beam cross sections for engineers. This program makes this process easier. Easy to use GUI and colorful stress analysis results helps engineers. My program is based on my unpublished mechanical engineering master thesis. You can find sample data here too. Save file is easy to edit as text file so optimization can easily be performed. -
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FUNseq
Cell segmentation/tracking for determing aggresive cancer phenotypes
This page shows the cell segmentation/tracking program for FUNseq pipeline. Identifying a sparse subset of cancer cells from a large heterogeneous population, based on aggressive phenotypes (like invasive migration, multipolar divisions, or asymmetric lineage development) is challenging. Also, such aberration identification is critical, as cells exhibiting these characteristics are linearly correlated with poor prognosis. A high-throughput screening microscope has been developed in our... -
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Sentiment dataset of Algerian dialect
Dataset of 11760 sentiment comments written in Algerian dialect
* To cite this dataset refer to https://doi.org/10.31449/inf.v46i6.3340 * This sentiment dataset of Algerian dialect consists of 11760 comments (6111 positive/ 5649 negative comments)) collected from (Facebook, YouTube and Twitter) during Hirak 2019. * Comments concern the Algerian spoken language, written in Arabic and/or Latin characters and/or Arabizi, which could be either Modern Standard Arabic, French or local dialect. * Value ‘1’ is attributed for Positive review / value ‘0’... -
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coDDMaker
distributions and co-distribution 2D signal analysis
coDDMaker is a MATLAB® App Designer's software program for the guided analysis of the distributions and co-distribution of marker pairs in 2D image. -
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GENET-CNV
Integrated DNA copy number variation and gene expression analysis
The Boolean implication networks outperformed Bayesian networks, Pearson’s correlation networks, and other Boolean networks in constructing genome-scale co-expression networks evaluated with comprehensive biological pathways and Gene Ontology in MSigDB. References: Guo NL, Wan YW. Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artificial Intelligence in Medicine 2012 Jun;55(2):97-105. Ye Q, Singh S, Qian PR, Guo... -
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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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...Final output barcodes can be used in identification of true variants with very low allele frequency less than or equal to 1% existing in liquid biopsy from cancers, quantitative transcriptome analysis to estimate accurate expression levels of genes or transcripts, and even single-cell sequencing of large cell populations. Operating system: Linux Programming language: C++ License: Non-Commercial Research Use Only
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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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LANDISVIEW 2.0
A tool to visualize, animate, analyze LANDIS images (.gis, .img, tiff)
LANDISVIEW 2.10 is a tool to visualize, animate and analyze LANDIS output maps (ERDAS Ver. 7.X GIS File Format - .gis, ERDAS IMAGINE File Format - .img). It can also convert LANDIS output maps into ASCII and batch files. LANDISVIEW 2.0 provides two major functions: File Viewer: Files can be viewed by adding them sequentially and an output can be generated as an image, an animation or a video. File converter: It will convert the loaded .gis or .img files for compatibility with...
