76 Open source projects that are alternatives of or similar to scGEAToolbox

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Reference mapping for single-cell genomics

R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)

Single cell type annotation guided by cell atlases, with freedom to be queer

SHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection

Examples using Clustergrammer2 to explore high-dimensional datasets.

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.

Tutorials, workflows, and convenience scripts for Single Cell Portal

BEER: Batch EffEct Remover for single-cell data

Clone identification from single-cell data

Demultiplexing pooled scRNA-seq data with or without genotype reference

Scripts demo-ing how to train a Word2Vec model and reduce its vector space

Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing

Spatial Transcriptomics Dashboard

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

CellExplorer is a graphical user interface, a standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes.

interactive Multi Objective K-mer Analysis

Papers with code for single cell related papers

Playing with MNIST. Machine Learning. Generative Models.

GREIN : GEO RNA-seq Experiments Interactive Navigator

Clustering scRNAseq by genotypes

Deep Learning API and Server in C++14 support for Caffe, Caffe2, PyTorch,TensorRT, Dlib, NCNN, Tensorflow, XGBoost and TSNE

Machine learning algorithm such as KNN,Naive Bayes,Logistic Regression,SVM,Decision Trees,Random Forest,k means and Truncated SVD on amazon fine food review

A tool for semi-automatic cell type annotation

Discover differential transcript usage from polyA-captured single cell RNA-seq data

Harmony framework for connecting scRNA-seq data from discrete time points

Google News and Leo Tolstoy: Visualizing Word2Vec Word Embeddings using t-SNE.

A tool for fast and accurate summarizing of variant calling format (VCF) files

Efficient and precise single-cell reference atlas mapping with Symphony

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Spatial alignment of single cell transcriptomic data.

Fast in-silico normalization algorithm for NGS data

Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

libmorph rus/ukr - fast & accurate morphological analyzer/analyses for Russian and Ukrainian

The World's First Search Engine for Trajectory Data

Make rapid visualizations of RNA-seq data in R

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Data-driven Network-based Bayesian Inference of Drivers

Inverse Kinematics Engine for the Franka Emika Panda for Cartesian Pose Control.

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Trajectory Tracking Project

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

Reconstruction of complex single-cell trajectories using CellRouter

Scalable RNA-seq analysis

Python package designed for collecting and processing trajectory data.

Parallel t-SNE implementation with Python and Torch wrappers.

Conversion between scRNA-seq objects

create "Karpathy's style" 2d images out of your image embeddings

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

Single-cell Hierarchical Poisson Factorization

Snakemake based pipeline for RNA-Seq analysis

Formed trajectories of sets of points.Experimented on finding similarities between trajectories based on DTW (Dynamic Time Warping) and LCSS (Longest Common SubSequence) algorithms.Modeled trajectories as strings based on a Grid representation.Benchmarked KNN, Random Forest, Logistic Regression classification algorithms to classify efficiently t…

Pega Data Scientist Tools

Imputation method for scRNA-seq based on low-rank approximation