Python Stem-cell-hypothesis Resources

Stem Player Player Stem Player Player Usage Download the latest release here Optional: install ffmpeg, instructions here NOTE: DOES NOT ENABLE DOWNLOA

MarcoPolo is a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering Overview MarcoPolo

scAR scAR (single cell Ambient Remover) is a package for denoising multiple single cell omics data. It can be used for multiple tasks, such as, sgRNA

The GT4SD (Generative Toolkit for Scientific Discovery) is an open-source platform to accelerate hypothesis generation in the scientific discovery process. It provides a library for making state-of-the-art generative AI models easier to use.

Hypothesis debugging with vscode

colab-xterm Colab-xterm allows you to open a terminal in a cell. Usage Install package and load the extension !pip install git+https://github.com/popc

STEM: An approach to Multi-source Domain Adaptation with Guarantees Introduction This is the official implementation of ``STEM: An approach to Multi-s

SegPC-2021 This is the official repository for the ISBI 2021 paper Transformer Assisted Convolutional Neural Network for Cell Instance Segmentation by

cell_counting_v2 The repository includes the code for training cell counting applications. (Keras + Tensorflow) Dataset can be downloaded here : http:

Rbc-traps-generative-design - The generative design for single red clood cell hydrodynamic traps using GEFEST framework

CellRank's reproducibility repository We believe that reproducibility is key and have made it as simple as possible to reproduce our results. Please e

FGHV Impelmentation for paper Feature Generation and Hypothesis Verification for Reliable Face Anti-Spoofing Requirements Python 3.6 Pytorch 1.5.0 Cud

Sartorius - Cell Instance Segmentation https://www.kaggle.com/c/sartorius-cell-instance-segmentation Environment setup Build docker image bash .dev_sc

GAN-STEM-Conv2MultiSlice GAN method to help covert lower resolution STEM images generated by convolution methods to higher resolution STEM images gene

excel-cell-checker Description This tool checks a given .xlsx file has the struc

Single-Cell Image Analysis Package Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spa

hypothesmith Hypothesis strategies for generating Python programs, something like CSmith. This is definitely pre-alpha, but if you want to play with i

A Parameter-free Deep Embedded Clustering Method for Single-cell RNA-seq Data Overview Clustering analysis is widely utilized in single-cell RNA-seque

Spatio-Temporal Entropy Model A Pytorch Reproduction of Spatio-Temporal Entropy Model (STEM) for end-to-end leaned video compression. More details can

h h is the web app that serves most of the https://hypothes.is/ website, including the web annotations API at https://hypothes.is/api/. The Hypothesis

unitcell Python script to generate vector graphics of an oriented lattice unit cell Examples unitcell --type hexagonal --eulers 12 23 34 --axes --crys

PyCellID (building...) Functions to analyze Cell-ID single-cell cytometry data using python language. Dependecies for this project. attrs(=21.1.0) fo

Implementation of the ivis algorithm as described in the paper Structure-preserving visualisation of high dimensional single-cell datasets.

The Lottery Ticket Hypothesis for Pre-trained BERT Networks Code for this paper The Lottery Ticket Hypothesis for Pre-trained BERT Networks. [NeurIPS

Structured Super Lottery Tickets in BERT This repo contains our codes for the paper "Super Tickets in Pre-Trained Language Models: From Model Compress

The Stem Cell Hypothesis Codes for our paper The Stem Cell Hypothesis: Dilemma behind Multi-Task Learning with Transformer Encoders published to EMNLP

ZePHyR: Zero-shot Pose Hypothesis Rating ZePHyR is a zero-shot 6D object pose estimation pipeline. The core is a learned scoring function that compare

MHFormer: Multi-Hypothesis Transformer for 3D Human Pose Estimation This repo is the official implementation of "MHFormer: Multi-Hypothesis Transforme

Scanpy – Single-Cell Analysis in Python Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It inc

Scripts for "Current best-practices in single-cell RNA-seq: a tutorial" This repository is complementary to the publication: M.D. Luecken, F.J. Theis,

Cellpose | A generalist algorithm for cell and nucleus segmentation. Cellpose was written by Carsen Stringer and Marius Pachitariu. To learn about Cel

Code for the paper "Generative Models and Model Criticism via Optimized Maximum Mean Discrepancy" (arXiv:1611.04488; published at ICLR 2017), by Douga

PhenoGraph for Python3 PhenoGraph is a clustering method designed for high-dimensional single-cell data. It works by creating a graph ("network") repr

A Python adaption of Augur to prioritize cell types in perturbation analysis.

Cellpose | A generalist algorithm for cell and nucleus segmentation. Cellpose was written by Carsen Stringer and Marius Pachitariu. To learn about Cel

Install vintools To download this package from pypi: pip install vintools Install the development package To download and install the developmen

Map single-cell transcriptomes to copy number evolutionary trees. Check out the tutorial for more information. Installation $ pip install scatrex SCA

You are caught stealing my winning lottery ticket! Making a lottery ticket claim its ownership Codes for [NeurIPS'21] You are caught stealing my winni

Drawing Robust Scratch Tickets: Subnetworks with Inborn Robustness Are Found within Randomly Initialized Networks Yonggan Fu, Qixuan Yu, Yang Zhang, S

pcnaDeep-napari A customized interface for single cell track visualisation based on pcnaDeep and napari. 👀 Under construction You can get test image

On Path Integration of Grid Cells: Group Representation and Isotropic Scaling This repo contains the official implementation for the paper On Path Int

A totally unrealistic cell growth/reproduction simulation.

Kaggle: Cell Instance Segmentation The goal of this challenge is to detect cells in microscope images. with simple view on how many cels have been ann

AMAZ3DSim AMAZ3DSim is a lightweight python-based 3D network multi-agent simulator. It uses a cell-based congestion model. It calculates risk, battery

starfish: scalable pipelines for image-based transcriptomics starfish is a Python library for processing images of image-based spatial transcriptomics

scBALF Covid-19 dataset Analysis Here is the Github page that has the codes for the bioinformatics pipeline described in the paper COVID-Datathon: Bio

LIVECell dataset This document contains instructions of how to access the data associated with the submitted manuscript "LIVECell - A large-scale data

Python package for probability density function fitting of univariate distributions of non-censored data

pcnaDeep: a deep-learning based single-cell cycle profiler with PCNA signal Welcome! pcnaDeep integrates cutting-edge detection techniques with tracki

CW Networks This repository contains the code used for the papers Weisfeiler and Lehman Go Cellular: CW Networks (Under review) and Weisfeiler and Leh

FunMatch-Distillation TF2 implementation of knowledge distillation using the "function matching" hypothesis from the paper Knowledge distillation: A g

ncem Features Repository for the manuscript Fischer, D. S., Schaar, A. C. and Theis, F. Learning cell communication from spatial graphs of cells. 2021

Scirpy: A Scanpy extension for analyzing single-cell immune-cell receptor sequencing data Scirpy is a scalable python-toolkit to analyse T cell recept

LTH-ObjectRecognition The Lottery Ticket Hypothesis for Object Recognition Sharath Girish*, Shishira R Maiya*, Kamal Gupta, Hao Chen, Larry Davis, Abh

kaggle-hpa-2021-7th-place-solution Code for 7th place solution of Human Protein Atlas - Single Cell Classification on Kaggle. A description of the met

The Lottery Tickets Hypothesis for Supervised and Self-supervised Pre-training in Computer Vision Models Codes for this paper The Lottery Tickets Hypo

The lottery ticket hypothesis (LTH) reveals the existence of winning tickets (sparse but critical subnetworks) for dense networks, that can be trained in isolation from random initialization to match the latter’s accuracies.

SHOT++ Code for our TPAMI submission "Source Data-absent Unsupervised Domain Adaptation through Hypothesis Transfer and Labeling Transfer" that is ext

wide-minima-density-hypothesis Details about the wide minima density hypothesis and metrics to compute width of a minima This repo presents the wide m

Interpretation of T cell states using reference single-cell atlases ProjecTILs is a computational method to project scRNA-seq data into reference sing

hyppo (HYPothesis Testing in PythOn, pronounced "Hippo") is an open-source software package for multivariate hypothesis testing.

deep-significance: Easy and Better Significance Testing for Deep Neural Networks Contents ⁉️ Why 📥 Installation 🔖 Examples Intermezzo: Almost Stocha

Ultra-Data-Efficient GAN Training: Drawing A Lottery Ticket First, Then Training It Toughly Code for this paper Ultra-Data-Efficient GAN Tra

Table of contents What is PEM? Overview Installation Usage Executable Library Telegram Bot Try OPEM in Your Browser! MATLAB Issues & Bug Reports Contr

an interactive explorer for single-cell transcriptomics data cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell tra

cochlea cochlea is a collection of inner ear models. All models are easily accessible as Python functions. They take sound signal as input and return

stempeg = stems + ffmpeg Python package to read and write STEM audio files. Technically, stems are audio containers that combine multiple audio stream

Schemathesis Schemathesis is a modern API testing tool for web applications built with Open API and GraphQL specifications. It reads the application s

Schemathesis Schemathesis is a modern API testing tool for web applications built with Open API and GraphQL specifications. It reads the application s

Hypothesis Hypothesis is a family of testing libraries which let you write tests parametrized by a source of examples. A Hypothesis implementation the

Schemathesis Schemathesis is a modern API testing tool for web applications built with Open API and GraphQL specifications. It reads the application s

Hypothesis Hypothesis is a family of testing libraries which let you write tests parametrized by a source of examples. A Hypothesis implementation the