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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support... -
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LP CSIC/UAB Apps and Code
Software and Code from Laboratori de Proteòmica CSIC/UAB
Software, Code and Documents from Laboratori de Proteòmica CSIC/UAB ( LP-CSIC/UAB: http://proteomica.uab.cat ) -
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Ligaturizer
Programming Fonts with Ligatures added
This script copies the ligatures (glyphs and rendering information) from Fira Code into any other TrueType or OpenType font. (Note that the ligatures are scale-corrected, but otherwise copied as is from Fira Code; it doesn't create new ligature graphics based on the font you're modifying.) This repo contains a Fontforge python script that you can use to add the Fira Code ligatures to any font, as well as submodules for some popular coding fonts and another script for ligaturizing all of them... -
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Xmaldi
Viewing collections of MALDI spectra and perform PCA and DFA analyses
Xmaldi is an application for viewing collections of MALDI spectra and perform PCA and DFA analyses on them (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/xmaldi3/code/ci/default/tree/README.md -
The AI workplace management platformBy combining AI workflows, predictive intelligence, and automated insights, OfficeSpace gives leaders a complete view of how their spaces are used and how people work. Facilities, IT, HR, and Real Estate teams use OfficeSpace to optimize space utilization, enhance employee experience, and reduce portfolio costs with precision.
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JSONVisor
Visor for mass spectrometry JSON files generated by Integrator
Visor for mass spectrometry JSON files generated by the Integrator program (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/jsonvisor3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. -
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HistogramsApp
Application that generates KDE-PDP plots from geochronological data
...P., Bonilla-Correa, S., Izquierdo-Camacho, D., ... & Montes, C. (2021). The Colombian geochronological database (CGD). International Geology Review, 1-35. And the Zenodo repository where the source code is available: 2) Rodriguez Corcho (2021). andresrcorcho/CGD_HistogramsApp: HistogramsApp_1.5 (1.5). Zenodo. https://doi.org/10.5281/zenodo.5171646 (https://zenodo.org/record/5171646#.YZ4X9r3P27M) -
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Vimplus
An automatic configuration program for vim
vimplus is an opinionated Vim “distribution” and automatic configuration program by chxuan which bundles a large number of plugins and configurations so that you can essentially install Vim once and have a fully-loaded development setup. Rather than starting with a bare .vimrc and gradually adding plugins, vimplus gives you a pre-configured environment that includes file explorers, completion, status lines, themes, and more. It includes a custom installer and update script, and places a lot... -
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Rescatux
Easy to use Repair distribution for both Gnu/Linux and Windows systems
Rescatux is a GNU/Linux repair cd (and eventually also Windows) but it is not like other rescue disks. Rescatux comes with Rescapp. Rescapp is a nice wizard that will guide you through your rescue and repair tasks. When the wizard is not able to solve your problem you can also enjoy of Rescatux unique support features: * Chat: Open the chat for asking help directly in Rescatux channel. * Share log: After running an option you can share its log (the action registry that it has done) so... -
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LaiaMotifs
Search for MHC-like motifs in peptide collections
Search for MHC-like motifs in peptide collections (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/laiamotifs3/code/ci/default/tree/README.md -
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django-webpack-dev-server
Commandline App to set up React in a Django Project with 1 command.
Django Webpack Dev Server is a command line Django reusable app to setup configuration files for React. It uses webpack and webpack_dev_server to bundle your frontend code. After installing the app you need to run the following command: "python manage.py generate react" and that will create your react app in your project. -
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restless
A lightweight REST miniframework for Python
...It also uses HTTP status codes as correctly as possible. Restless is BYOD (bring your own data) and hence, works with almost any ORM/data source. If you can import a module to work with the data & can represent it as JSON, Restless can work with it. Restless is small & easy to keep in your head. Common usages involve overriding just a few easily remembered method names. Total source code is an under a thousand lines of code. -
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Blade Build System
Blade is a powerful build system from Tencent
An easy-to-use, fast and modern build system for trunk-based development in large-scale mono repo codebase. The code on the master branch is the development version and should be considered as alpha version. Please prefer using the version on the tags in your formal environment. We will release the verified version on the large-scale internal code base to the tag from time to time. -
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Tez
Tez is a super-simple and lightweight Trainer for PyTorch
Tez is a super-simple and lightweight Trainer for PyTorch. It also comes with many utils that you can use to tackle over 90% of deep learning projects in PyTorch. tez (तेज़ / تیز) means sharp, fast & active. This is a simple, to-the-point, library to make your PyTorch training easy. This library is in early-stage currently! So, there might be breaking changes. Currently, tez supports cpu, single gpu and multi-gpu & tpu training. More coming soon! Using tez is super-easy. We don't want you to... -
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gpt-j-api
API for the GPT-J language mode. Including a FastAPI backend
An API to interact with the GPT-J language model and variants! You can use and test the model in two different ways. These are the endpoints of the public API and require no authentication. Just SSH into a TPU VM. This code was tested on both the v2-8 and v3-8 variants. -
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KimBlast
Blast+ the easy way
KimBlast GUI formats and indexes Fasta databases for Blast, performs Blast searches and analyzes results. Python 3.x version. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimblast3/code/ci/default/tree/README.md -
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Pytago
A source-to-source transpiler for Python to Go translation
pytago is a source-to-source transpiler that converts some Python into human-readable Go. It enables developers to translate Python codebases into Go, facilitating migration or interoperability between the two languages. -
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aseryla
Aseryla code repositories
This project describes a model of how the semantic human memory represents the information relevant to the objects of the world in text format. It provides a system and a GUI application capable of extracting and managing concepts and relations from English texts. https://aseryla2.sourceforge.io/ -
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CleverHans
An adversarial example library for constructing attacks
This repository contains the source code for CleverHans, a Python library to benchmark machine learning systems' vulnerability to adversarial examples. You can learn more about such vulnerabilities on the accompanying blog. The CleverHans library is under continual development, always welcoming contributions of the latest attacks and defenses. In particular, we always welcome help with resolving the issues currently open. -
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ReinventCommunity
Jupyter Notebook tutorials for REINVENT 3.2
This repository is a collection of useful jupyter notebooks, code snippets and example JSON files illustrating the use of Reinvent 3.2. -
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Old Photo Restoration
Bringing Old Photo Back to Life (CVPR 2020 oral)
We propose to restore old photos that suffer from severe degradation through a deep learning approach. Unlike conventional restoration tasks that can be solved through supervised learning, the degradation in real photos is complex and the domain gap between synthetic images and real old photos makes the network fail to generalize. Therefore, we propose a novel triplet domain translation network by leveraging real photos along with massive synthetic image pairs. Specifically, we train two... -
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Pythopad
A free Python source code editor and Notepad replacement for Windows
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Neuro-comma
Punctuation restoration production-ready model for Russian language
This library was developed with the idea to help us to create punctuation restoration models to memorize trained parameters, data, training visualization, etc. The Library doesn't use any high-level frameworks, such as PyTorch-lightning or Keras, to reduce the level entry threshold. Feel free to fork this repo and edit model or dataset classes for your purposes. Our team always uses the latest version and features of Python. We started with Python 3.9, but realized, that there is no FastAPI... -
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U-Net Fusion RFI
U-Net for RFI Detection based on @jakeret's implementation
See original code here: https://github.com/jakeret/tf_unet Currently this project is based on Tensorflow 1.13 code base and there are no plans to transfer to TF version 2. The primary improvements to this code base include a training and evaluation framework, along with a fusion based approach to detection, combining a number of models (currently hard coded to two trained models) along with Sum Threshold as an additional "expert." Additional work is being done to add custom layers to... -
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ClamGuard
Free and opensource antivirus solution based on ClamAV.
Free and opensource antivirus solution based on ClamAV. Fully written in Python using PySide6. Source code hosted on GitHub at https://github.com/5trange/ClamGuard Linux packages coming soon. -
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ML workspace
All-in-one web-based IDE specialized for machine learning
All-in-one web-based development environment for machine learning. The ML workspace is an all-in-one web-based IDE specialized for machine learning and data science. It is simple to deploy and gets you started within minutes to productively built ML solutions on your own machines. This workspace is the ultimate tool for developers preloaded with a variety of popular data science libraries (e.g., Tensorflow, PyTorch, Keras, Sklearn) and dev tools (e.g., Jupyter, VS Code, Tensorboard)...
