broadinstitute/single_cell_portal_core

Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

Language: Ruby - Size: 37.8 MB - Last synced: about 19 hours ago - Pushed: about 20 hours ago - Stars: 60 - Forks: 25

showteeth/scfetch

Access and Format Single-cell RNA-seq Datasets from Public Resources

Language: R - Size: 4.52 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 23 - Forks: 2

satijalab/seurat

R toolkit for single cell genomics

Language: R - Size: 77.6 MB - Last synced: 3 days ago - Pushed: 6 days ago - Stars: 2,134 - Forks: 886

FertigLab/CoGAPS

Bayesian MCMC matrix factorization algorithm

Language: C++ - Size: 250 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 53 - Forks: 16

stemangiola/CuratedAtlasQueryR

Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.

Language: R - Size: 8.84 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 75 - Forks: 6

iSEE/iSEE

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

Language: R - Size: 16.4 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 220 - Forks: 41

federicomarini/HCAData

Access data from the Human Cell Atlas project, directly via R/Bioconductor

Language: R - Size: 7.37 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 8 - Forks: 2

Comparative-Pathology/comparativepathologyworkbench

Comparative Pathology Workbench

Language: Python - Size: 41.9 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 0

spacetx/upload-validator

HumanCellAtlas upload-service validator for SpaceTx files

Language: Makefile - Size: 1000 Bytes - Last synced: 15 days ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

satijalab/seurat-docker

Docker images of Seurat

Language: Dockerfile - Size: 52.7 KB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 8 - Forks: 7

theislab/cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

Language: Python - Size: 54 MB - Last synced: 12 days ago - Pushed: about 2 months ago - Stars: 74 - Forks: 15

theislab/scarches

Reference mapping for single-cell genomics

Language: Jupyter Notebook - Size: 784 MB - Last synced: 1 day ago - Pushed: about 1 month ago - Stars: 310 - Forks: 49

Teichlab/Genes2Genes

Aligning gene expression trajectories of single-cell reference and query systems

Language: Jupyter Notebook - Size: 31.3 MB - Last synced: 10 days ago - Pushed: 27 days ago - Stars: 17 - Forks: 3

broadinstitute/single_cell_portal

Tutorials, workflows, and convenience scripts for Single Cell Portal

Language: HTML - Size: 128 MB - Last synced: 27 days ago - Pushed: 2 months ago - Stars: 45 - Forks: 24

scverse/scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Language: Python - Size: 135 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1,113 - Forks: 336

spacetx/starfish

starfish: unified pipelines for image-based transcriptomics

Language: Python - Size: 114 MB - Last synced: 22 days ago - Pushed: about 2 months ago - Stars: 220 - Forks: 66

iSEE/iSEE_custom

Examples of custom panels for the iSEE package

Language: R - Size: 3.41 MB - Last synced: 7 days ago - Pushed: over 4 years ago - Stars: 6 - Forks: 1

rachadele/download-geo-fastqs

Download fastqs or supplementary files from GEO and upload to hca-util bucket

Language: Shell - Size: 77.1 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

tallulandrews/M3Drop

Language: R - Size: 5.51 MB - Last synced: 7 days ago - Pushed: 2 months ago - Stars: 28 - Forks: 9

hemberg-lab/SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

Language: R - Size: 13.5 MB - Last synced: 6 days ago - Pushed: almost 3 years ago - Stars: 115 - Forks: 55

MarioniLab/scran

Clone of the Bioconductor repository for the scran package.

Language: R - Size: 2.85 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 37 - Forks: 22

LTLA/MoeDCPLogo

Making the DCP logo moe-r.

Size: 3.01 MB - Last synced: 2 months ago - Pushed: about 5 years ago - Stars: 8 - Forks: 0

LTLA/batchelor

Clone of the Bioconductor repository for the batchelor package.

Language: R - Size: 802 KB - Last synced: 2 months ago - Pushed: 5 months ago - Stars: 18 - Forks: 7

LTLA/BiocNeighbors

Clone of the Bioconductor repository for the BiocNeighbors package.

Language: C++ - Size: 653 KB - Last synced: 2 months ago - Pushed: 4 months ago - Stars: 6 - Forks: 10

drisso/SingleCellExperiment

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.

Language: R - Size: 445 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 61 - Forks: 17

lasersonlab/zappy 📦

Distributed processing with NumPy and Zarr

Language: Python - Size: 106 KB - Last synced: 18 days ago - Pushed: over 5 years ago - Stars: 9 - Forks: 2

MarioniLab/DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

Language: R - Size: 590 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 53 - Forks: 25

nlawlor/PBMC_CITEseq

CITE-seq profiling of human PBMCs at baseline and activation conditions

Language: R - Size: 919 KB - Last synced: 2 months ago - Pushed: 8 months ago - Stars: 4 - Forks: 1

spacetx/spacetx-writer

Convert supported filesets to the SpaceTx format

Language: Java - Size: 85.9 KB - Last synced: 15 days ago - Pushed: about 5 years ago - Stars: 3 - Forks: 1

MarioniLab/EmptyDrops2017

Code for the empty droplet and cell detection project from the HCA Hackathon.

Language: TeX - Size: 531 KB - Last synced: 2 months ago - Pushed: about 5 years ago - Stars: 18 - Forks: 4

hemberg-lab/scmap

A tool for unsupervised projection of single cell RNA-seq data

Language: R - Size: 3.84 MB - Last synced: 6 months ago - Pushed: over 3 years ago - Stars: 86 - Forks: 13

lasersonlab/ndarray.scala

N-dimensional arrays, with Zarr and HDF5 integrations

Language: Scala - Size: 9.53 MB - Last synced: 4 months ago - Pushed: about 5 years ago - Stars: 14 - Forks: 3

quon-titative-biology/scBFA

Binary Factor Analysis: a dimensionality reduction tool for noisy, high throughput single cell genomic data

Language: R - Size: 4.4 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 2

LuyiTian/sc_mixology

This contains the dataset for comparing scRNA-seq analysis methods

Language: HTML - Size: 368 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 80 - Forks: 27

quon-titative-biology/scAlign

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

Language: R - Size: 5.18 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 32 - Forks: 12

morris-lab/CellTagR

This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.

Language: R - Size: 39 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 16 - Forks: 6

chanzuckerberg/ontology-ui

Ontology visualizer

Language: TypeScript - Size: 12.4 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 6 - Forks: 0

tatami-inc/beachmat

Clone of the Bioconductor repository for the beachmat package.

Language: C++ - Size: 1.83 MB - Last synced: 7 days ago - Pushed: about 2 months ago - Stars: 4 - Forks: 5

hemberg-lab/D3E

Discrete Distributional Differential Expression

Language: Python - Size: 50.8 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 22 - Forks: 9

Bioconductor/HCAExplorer

CURRENTLY IN DEVELOPMENT. A package to provide user-friendly access to Human Cell Atlas resources. This package is meant to have similar functionality to the HCA data-explorer https://data.humancellatlas.org/explore/projects.

Language: R - Size: 76.2 KB - Last synced: 7 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

Bioconductor/HCABrowser

Browse the Human Cell Atlas data portal

Language: R - Size: 516 KB - Last synced: 7 days ago - Pushed: about 1 year ago - Stars: 8 - Forks: 4

Bioconductor/HCAMatrixBrowser

:warning: DEPRECATED :warning: Download Matrix Data using the HCA API

Language: R - Size: 93.8 KB - Last synced: 7 days ago - Pushed: about 1 year ago - Stars: 3 - Forks: 0

drisso/mbkmeans

K-means clustering for large single-cell datasets

Language: R - Size: 5.89 MB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 9 - Forks: 3

morris-lab/BiddyetalWorkflow

This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.

Language: R - Size: 14.6 MB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 23 - Forks: 10

LTLA/BiocSingular

Clone of the Bioconductor repository for the BiocSingular package.

Language: R - Size: 248 KB - Last synced: 8 days ago - Pushed: 3 months ago - Stars: 6 - Forks: 1

lasersonlab/single-cell-experiments

Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark

Language: Jupyter Notebook - Size: 7.98 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 13 - Forks: 8

NElnour/CAPSULE

An R package that visualizes Human Cell Atlas annotations on an SVG cell image.

Language: R - Size: 2.96 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

broadinstitute/2018_04_20_Rosetta

Translating morphology data across single-cell modalities (CZI)

Language: Jupyter Notebook - Size: 40.2 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 2

morris-lab/PreviousCloneHunter

This repository contains our CellTag CloneHunter R package for clone-calling.

Language: R - Size: 30.4 MB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 6 - Forks: 2

jenni-westoby/ES_cell_pipeline

Benchmarking pipeline published in https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1571-5

Language: R - Size: 7.81 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 1

jenni-westoby/Drop-seq_pipeline

This is the pipeline to perform a Drop-seq simulation based benchmark - see https://www.biorxiv.org/content/early/2018/01/17/248716

Language: Shell - Size: 5.1 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0

morris-lab/CellTagViz

Repository of the CellTag Viz Shiny App

Language: HTML - Size: 13.8 MB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

jenni-westoby/BLUEPRINT

Benchmarking pipeline published in https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1571-5

Language: R - Size: 5.65 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 1

lasersonlab/scsearch

Index and search single cell data.

Language: Java - Size: 15.6 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0