1081 Open source projects that are alternatives of or similar to scarf

A comprehensive dimensional reduction framework to recover the latent topology from high-dimensional data.

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

<<------ Use SnapATAC!!

BEER: Batch EffEct Remover for single-cell data

Reference mapping for single-cell genomics

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

Workshop (6 hours): Clustering (Hdbscan, LCA, Hopach), dimension reduction (UMAP, GLRM), and anomaly detection (isolation forests).

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

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

Spatial Single Cell Analysis in Python

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

Papers with code for single cell related papers

Version 2.1.0 released

Differential expression analysis for single-cell RNA-seq data.

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

CellRank for directed single-cell fate mapping

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Discrete Distributional Differential Expression

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Using machine learning on your anki collection to enhance the scheduling via semantic clustering and semantic similarity

A fast, scalable and light-weight C++ Fréchet distance library, exposed to python and focused on (k,l)-clustering of polygonal curves.

Clustering scRNAseq by genotypes

MooseFS – Open Source, Petabyte, Fault-Tolerant, Highly Performing, Scalable Network Distributed File System (Software-Defined Storage)

Hazelcast IMDG C++ Client

Hazelcast IMDG Node.js Client

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

Hazelcast IMDG Python Client

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

All-in-one analysis pipeline

C4E, a JVM friendly library written in Scala for both local and distributed (Spark) Clustering.

Implementation of the k-means algorithm in PyTorch that works for large datasets

A R framework for pipeline benchmarking, with application to single-cell RNAseq

Hazelcast IMDG Go Client

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

Hazelcast .NET Client

Proto Actor - Ultra fast distributed actors

Apache Spark Data Source for ROOT File Format

Automatic feature engineering using Generative Adversarial Networks using Deeplearning4j and Apache Spark.

Examples to get started with IBM Functional Genomics Platform

A distributed in-memory key-value storage for billions of small objects.

Automile offers a simple, smart, cutting-edge telematics solution for businesses to track and manage their business vehicles.

Distributed stream processing model and its implementation

phenol: Phenotype ontology library

A python-based time series aggregation module (tsam) which can be used to reduce the number of time steps using typical periods or by decreasing the temporal resolution

High level linear algebra library for Dlang

Improve the quality of a denovo assembly by scaffolding and gap filling

Analysis kit for large-scale structure datasets, the massively parallel way

A collection of 50+ trajectory inference methods within a common interface 📥📤

Manhattan plot Generator

High performance t-SNE for Ruby

A distributed, fast open-source graph database featuring horizontal scalability and high availability

Analysing Capture Seq Count Data

CUT&RUN and CUT&Tag data processing and analysis

An implementation of "Community Preserving Network Embedding" (AAAI 2017)

Easily turn large sets of image urls to an image dataset. Can download, resize and package 100M urls in 20h on one machine.

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Introduction to the Command Line for Genomics

DevOps pipeline for Real Time Social/Web Mining

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

The Proteomics Experimental Design file format: Standard for experimental design annotation