Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: single-cell-genomics

Repositories

vertesy/Seurat.utils

Various utility functions for Seurat single-cell analysis

Language: R - Size: 2.78 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 26 - Forks: 6

satijalab/seurat-wrappers

Community-provided extensions to Seurat

Language: R - Size: 116 MB - Last synced: about 13 hours ago - Pushed: 1 day ago - Stars: 284 - Forks: 126

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 20 hours ago - Pushed: about 21 hours ago - Stars: 60 - Forks: 25

dpeerlab/Palantir

Single cell trajectory detection

Language: Jupyter Notebook - Size: 55.7 MB - Last synced: about 11 hours ago - Pushed: about 21 hours ago - Stars: 195 - Forks: 45

kaizhang/SnapATAC2

Single-cell epigenomics analysis tools

Language: Python - Size: 24.9 MB - Last synced: about 22 hours ago - Pushed: 1 day ago - Stars: 177 - Forks: 19

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

amsesk/SCGid

SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries

Language: Python - Size: 11 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 3

pinellolab/pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

Language: Python - Size: 21.8 MB - Last synced: 6 days ago - Pushed: 17 days ago - Stars: 35 - Forks: 5

EngreitzLab/gene_network_evaluation

Evaluation framework for computationally inferred gene networks from single-cell data.

Language: Jupyter Notebook - Size: 77.3 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 7 - Forks: 6

scverse/squidpy

Spatial Single Cell Analysis in Python

Language: Python - Size: 9.43 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 392 - Forks: 71

satijalab/azimuth

A Shiny web app for mapping datasets using Seurat v4

Language: HTML - Size: 7.51 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 96 - Forks: 25

LiQian-XC/sctour

A deep learning architecture for robust inference and accurate prediction of cellular dynamics

Language: Python - Size: 5.8 MB - Last synced: about 19 hours ago - Pushed: 9 months ago - Stars: 45 - Forks: 3

byzhang23/TreeCorTreat

TreeCorTreat

Language: R - Size: 43.3 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 6 - Forks: 0

jsxlei/SCALEX

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

Language: Jupyter Notebook - Size: 4.96 MB - Last synced: 3 days ago - Pushed: 14 days ago - Stars: 67 - Forks: 19

ytanaka-bio/scIDST

Inference of Disease Progressive Level in Single-Cell Data

Language: Python - Size: 969 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 3 - Forks: 0

satijalab/seurat-data

Dataset distribution for Seurat

Language: R - Size: 184 KB - Last synced: 4 days ago - Pushed: 6 months ago - Stars: 112 - Forks: 43

theislab/cellrank

CellRank: dynamics from multi-view single-cell data

Language: Python - Size: 84.9 MB - Last synced: 8 days ago - Pushed: 23 days ago - Stars: 305 - Forks: 38

coldham10/SCarborSNV

SCarborSNV is an efficient algorithm for phylogeny aware genotyping of single cell genomes, using dynamic programming and neighbor joining.

Language: C - Size: 25.3 MB - Last synced: 18 days ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

theislab/scgen

Single cell perturbation prediction

Language: Python - Size: 69 MB - Last synced: 18 days ago - Pushed: 8 months ago - Stars: 247 - Forks: 51

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

enblacar/SCpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.

Language: R - Size: 87.6 MB - Last synced: 10 days ago - Pushed: 3 months ago - Stars: 130 - Forks: 10

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

parashardhapola/scarf

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.

Language: Python - Size: 32.6 MB - Last synced: 21 days ago - Pushed: 4 months ago - Stars: 89 - Forks: 12

Qile0317/APackOfTheClones

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.

Language: R - Size: 168 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 13 - Forks: 1

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

samuel-marsh/scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Language: R - Size: 276 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 163 - Forks: 19

maxplanck-ie/Rseurat

Single Cell RNA-seq Course

Language: R - Size: 17.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

lcrawlab/callback

Calibrated clustering via knockoffs for single-cell genomics

Language: R - Size: 6.53 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 6 - Forks: 0

perslab/timshel-2020

Code to reproduce analysis and figures for 'Genetic mapping of etiologic brain cell types for obesity' (Timshel, eLife 2020)

Language: R - Size: 347 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 13 - Forks: 4

10XGenomics/loupeR

Convert Seurat objects to 10x Genomics Loupe files.

Language: R - Size: 47.9 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 58 - Forks: 8

aron0093/gene_network_evaluation

Evaluation framework for computationally inferred gene networks from single-cell data.

Language: Python - Size: 7.4 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

jebard/ACED

ACED

Language: R - Size: 201 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

zhanghao-njmu/SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Language: R - Size: 788 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 284 - Forks: 54

microsoft/Nclusion.jl

Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data

Language: Julia - Size: 107 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 16 - Forks: 0

chenweng1991/redeemR

R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.

Language: Jupyter Notebook - Size: 11.5 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 8 - Forks: 2

HelloWorldLTY/AWGAN

Codes for paper: AWGAN: A Powerful Batch Effect Removal Model for scRNA-seq Data

Language: Jupyter Notebook - Size: 79.1 MB - Last synced: 11 days ago - Pushed: over 1 year ago - Stars: 7 - Forks: 0

WeiqiangZhou/BIRD

Big data Regression for predicting DNase I hypersensitivity

Language: C++ - Size: 10.9 MB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 29 - Forks: 5

ToureLaminelab/RNAvelocity

RNA velocity is a high-dimensional vector that predicts the future state of individual cells on a timescale of hours.

Language: Jupyter Notebook - Size: 43.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

calico/scnym

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

Language: Python - Size: 4.76 MB - Last synced: 2 days ago - Pushed: 5 months ago - Stars: 73 - Forks: 12

powellgenomicslab/ascend

Analysis of Single Cell Expression, Normalization and Differential expression

Language: R - Size: 11 MB - Last synced: 22 days ago - Pushed: about 4 years ago - Stars: 12 - Forks: 11

mojaveazure/loomR

An R-based interface for loom files

Language: R - Size: 327 KB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 58 - Forks: 14

mojaveazure/seurat-disk

Interfaces for HDF5-based Single Cell File Formats

Language: R - Size: 551 KB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 118 - Forks: 42

r3fang/snATAC

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

Language: Python - Size: 104 MB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 25 - Forks: 10

yanwu2014/swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

Language: R - Size: 211 MB - Last synced: 3 months ago - Pushed: 10 months ago - Stars: 103 - Forks: 21

p4rkerw/Wilson_GBio_2024

Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease

Language: R - Size: 4.58 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

Hon-lab/pySpade

Single cell Perturbations - Analysis of Differential gene Expression

Language: Python - Size: 805 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

ddiez/singleCellHaystack-py

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

Language: Python - Size: 69 MB - Last synced: 4 days ago - Pushed: 4 months ago - Stars: 8 - Forks: 1

neurogenomics/RareDiseasePrioritisation

Prioritise cell-type-specific gene targets from the Rare Disease Celltyping project.

Language: HTML - Size: 77.9 MB - Last synced: 7 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

LamineTourelab/SingleCell-rnaseq-tools

This repository contains single cell analysis pipelines.

Language: Jupyter Notebook - Size: 1.91 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

GuangyuWangLab2021/cellDancer

Predict RNA velocity through deep learning

Language: Jupyter Notebook - Size: 764 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 46 - Forks: 10

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

KChen-lab/SiFit

Reconstructing phylogenetic tree from noisy mutation profile of single cells

Size: 24.7 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 2

ManuSetty/Palantir 📦

Single cell trajectory detection

Language: Jupyter Notebook - Size: 11.8 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 3 - Forks: 1

Related Keywords

single-cell-genomics 86 single-cell-rna-seq 34 single-cell 28 single-cell-analysis 18 scrna-seq 14 bioinformatics 13 r 10 deep-learning 9 human-cell-atlas 9 clustering 8 seurat 8 single-cell-atac-seq 7 machine-learning 6 scrna-seq-analysis 6 single-cell-omics 6 transcriptomics 5 genomics 5 rna-seq 5 visualization 4 python 3 rna-seq-analysis 3 cell-fate-transitions 3 single-cell-sequencing 3 spatial-transcriptomics 3 data-visualization 3 single-cell-multiomics 3 dimensionality-reduction 3 rna-velocity 3 manifold-learning 3 gene-expression 3 trajectory-generation 3 shiny-apps 3 scrnaseq 3 multiomics 3 datasets 2 data-science 2 genetics 2 cancer-genomics 2 scvelo 2 clonal-analysis 2 computational-biology 2 velocity 2 generative-model 2 ggplot2 2 segmentation 2 single-cell-crispr-screening 2 data-integration 2 cite-seq 2 hdf5 2 mutation 2 transposon 2 scatac-seq 2 differential-expression 2 shiny 2 shiny-app 2 cell-fate-determination 2 rna-splicing 2 pseudotime 2 bioinformatics-pipeline 2 diffusion-maps 2 gene-regulatory-network 2 bioinformatics-tool 2 differentiation 2 deep-generative-model 2 rna-splicing-analysis 2 gene-co-expression-network 2 rna-velocity-estimation 2 enhancer-prediction 2 dna 1 manifold-learing 1 slurm 1 pipeline 1 alignment 1 indrops 1 star 1 chromosome-abberations 1 fair-data 1 sequencing 1 label-refinement 1 bioc2018 1 bioconductor 1 lineage-trajectory 1 normalization 1 kidney 1 loss-of-y-chromosome 1 mosaic-chromosomal-alterations 1 somatic-mosaicism 1 statistical-models 1 spatial-genomics 1 aav 1 celltypes 1 clinical-research 1 singularity 1 containerization 1 rare-disease 1 tenxgenomics 1 cellrank 1 expimap 1 rnavelocity 1 cell-fate 1