single-cell-analysis | Topic | Ecosyste.ms: Repos

Topic: "single-cell-analysis"

sqjin/CellChat 📦

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

Language: R - Size: 45.4 MB - Last synced at: 29 days ago - Pushed at: over 1 year ago - Stars: 693 - Forks: 158

jinworks/CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

Language: R - Size: 71.5 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 403 - Forks: 68

satijalab/seurat-wrappers

Community-provided extensions to Seurat

Language: R - Size: 121 MB - Last synced at: 5 days ago - Pushed at: 6 months ago - Stars: 332 - Forks: 136

DingWB/PyComplexHeatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

Language: Python - Size: 359 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 320 - Forks: 34

r3fang/SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

Language: R - Size: 170 MB - Last synced at: 19 days ago - Pushed at: about 2 years ago - Stars: 317 - Forks: 131

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 at: 12 months ago - Pushed at: about 1 year ago - Stars: 315 - Forks: 66

slowkow/harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

Language: Python - Size: 2.77 MB - Last synced at: 6 days ago - Pushed at: 11 months ago - Stars: 218 - Forks: 24

sunduanchen/Scissor

Scissor package

Language: C++ - Size: 28.5 MB - Last synced at: 6 months ago - Pushed at: about 1 year ago - Stars: 191 - Forks: 33

kharchenkolab/numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

Language: R - Size: 390 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 181 - Forks: 24

quadbio/scRNAseq_analysis_vignette

Tutorial for scRNA-seq data analysis beginners using R

Size: 243 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 177 - Forks: 63

pwwang/scplotter

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

Language: R - Size: 86.9 MB - Last synced at: 5 days ago - Pushed at: 13 days ago - Stars: 156 - Forks: 18

pinellolab/dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

Language: Python - Size: 25 MB - Last synced at: 19 days ago - Pushed at: 9 months ago - Stars: 117 - Forks: 14

dynverse/dynmethods

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

Language: R - Size: 18.9 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 114 - Forks: 26

GregorySchwartz/too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.

Language: Haskell - Size: 22.3 MB - Last synced at: 3 days ago - Pushed at: 7 months ago - Stars: 111 - Forks: 18

yanwu2014/swne

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

Language: R - Size: 211 MB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 105 - Forks: 19

powellgenomicslab/Nebulosa

R package to visualize gene expression data based on weighted kernel density estimation

Language: R - Size: 264 KB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 103 - Forks: 12

singleron-RD/CeleScope

Single Cell Analysis Pipelines

Language: Python - Size: 9.71 MB - Last synced at: about 17 hours ago - Pushed at: about 18 hours ago - Stars: 102 - Forks: 34

JEFworks-Lab/HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

Language: R - Size: 52.8 MB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 96 - Forks: 31

labsyspharm/scimap

Spatial Single-Cell Analysis Toolkit

Language: Python - Size: 43.3 MB - Last synced at: 5 days ago - Pushed at: 13 days ago - Stars: 91 - Forks: 31

gao-lab/SLAT

Spatial-Linked Alignment Tool

Language: Python - Size: 334 MB - Last synced at: 1 day ago - Pushed at: 5 months ago - Stars: 86 - Forks: 10

chriscainx/mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

Language: Python - Size: 1.05 MB - Last synced at: 13 days ago - Pushed at: over 2 years ago - Stars: 74 - Forks: 32

dynverse/dyngen

Simulating single-cell data using gene regulatory networks 📠

Language: HTML - Size: 607 MB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 73 - Forks: 6

sankaranlab/SCAVENGE

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

Language: R - Size: 38.5 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 73 - Forks: 34

a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

Language: Python - Size: 5.59 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 64 - Forks: 6

poseidonchan/TAPE

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

Language: Jupyter Notebook - Size: 161 MB - Last synced at: 26 days ago - Pushed at: about 1 year ago - Stars: 54 - Forks: 11

MannLabs/scPortrait

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

Language: Python - Size: 552 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 45 - Forks: 4

genecell/COSG

Accurate and fast cell marker gene identification with COSG

Language: Python - Size: 68.8 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 44 - Forks: 8

wanglab-broad/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 171 MB - Last synced at: 6 months ago - Pushed at: 10 months ago - Stars: 41 - Forks: 11

theislab/pseudodynamics

Dynamic models for single-cell RNA-seq time series.

Language: Jupyter Notebook - Size: 31.9 MB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 39 - Forks: 6

RabadanLab/randomly

A Library for Denoising Single-Cell Data with Random Matrix Theory

Language: Jupyter Notebook - Size: 4.52 MB - Last synced at: 3 days ago - Pushed at: almost 2 years ago - Stars: 37 - Forks: 10

berenslab/umi-normalization

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

Language: Jupyter Notebook - Size: 89.2 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 37 - Forks: 2

single-cell-genetics/XClone

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.

Language: Python - Size: 4.41 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 36 - Forks: 5

quadbio/scMultiome_analysis_vignette

Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis

Size: 26.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 33 - Forks: 9

nasqar/seuratv3wizard

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3

Language: R - Size: 10.9 MB - Last synced at: 20 days ago - Pushed at: over 4 years ago - Stars: 33 - Forks: 14

KChen-lab/bindSC

Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data

Language: R - Size: 48.1 MB - Last synced at: 12 months ago - Pushed at: almost 2 years ago - Stars: 31 - Forks: 7

YangLabHKUST/Portal

Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets

Language: Python - Size: 119 KB - Last synced at: 4 days ago - Pushed at: almost 2 years ago - Stars: 30 - Forks: 6

xzhoulab/DRComparison

Comparison of dimensionality reduction methods

Language: R - Size: 92.9 MB - Last synced at: 19 days ago - Pushed at: about 5 years ago - Stars: 30 - Forks: 10

quadbio/simspec

Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)

Language: R - Size: 8.08 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 27 - Forks: 3

SGI-LungCancer/SingleCell

Code repository for single cell RNA-seq

Language: R - Size: 16.1 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 27 - Forks: 11

ciccalab/SIMPLI

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

Language: R - Size: 45.2 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 26 - Forks: 4

paulranum11/SPLiT-Seq_demultiplexing

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

Language: Python - Size: 6.83 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 25 - Forks: 9

r3fang/snATAC

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

Language: Python - Size: 104 MB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 25 - Forks: 10

jumphone/BEER

BEER: Batch EffEct Remover for single-cell data

Language: R - Size: 60.1 MB - Last synced at: 16 days ago - Pushed at: 5 months ago - Stars: 24 - Forks: 9

arogozhnikov/demuxalot

Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing

Language: Python - Size: 2.5 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 24 - Forks: 3

KChen-lab/SCMER

Marker Selection by matching manifolds and elastic net

Language: HTML - Size: 192 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 23 - Forks: 4

zjunlp/ChatCell

ChatCell: Facilitating Single-Cell Analysis with Natural Language

Language: Python - Size: 17 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 3

nadeemlab/SPT

Spatial profiling toolbox for spatial characterization of tissue microenvironment (https://oncopathtk.org)

Language: Python - Size: 53.7 MB - Last synced at: 8 days ago - Pushed at: 15 days ago - Stars: 22 - Forks: 2

huBioinfo/CytoCommunity

A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from cell phenotypes.

Language: Python - Size: 202 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 21 - Forks: 13

bioturing/signac

An analytics package for single cell data

Language: C++ - Size: 23.4 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 21 - Forks: 5

WPZgithub/CEFCON

Deciphering driver regulators of cell fate decisions from single-cell RNA-seq data

Language: Jupyter Notebook - Size: 64.7 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 20 - Forks: 3

zjunlp/InstructCell

A Multi-Modal AI Copilot for Single-Cell Analysis with Instruction Following

Language: Jupyter Notebook - Size: 10.7 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 19 - Forks: 0

IGS/gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

Language: Jupyter Notebook - Size: 241 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 16 - Forks: 5

NIH-NEI/SCassist

SCassist : An AI Based Workflow Assistant for Single-Cell Analysis

Language: HTML - Size: 24.2 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 16 - Forks: 3

huidongchen/simba

SIMBA: SIngle-cell eMBedding Along with features

Language: Python - Size: 2.75 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 16 - Forks: 1

eudoraleer/scasa

SCASA: Single cell transcript quantification tool

Language: R - Size: 27.9 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 4

LucasESBS/vega

VEGA: VAE Enhanced by Gene Annotations

Language: Python - Size: 26.1 MB - Last synced at: 17 days ago - Pushed at: about 3 years ago - Stars: 15 - Forks: 2

harbourlab/PieParty

represent each cell in UMAP plots as a pie chart

Language: Python - Size: 20.3 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 14 - Forks: 1

AI4SCR/MatchCLOT

Python package implementing our method MatchCLOT for multimodal single-cell data integration

Language: Jupyter Notebook - Size: 8.36 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 13 - Forks: 3

dibbelab/gficf

An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

Language: C++ - Size: 4.89 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 15

nasqar/SeuratWizard

This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.

Language: R - Size: 8.77 MB - Last synced at: 20 days ago - Pushed at: over 5 years ago - Stars: 13 - Forks: 5

CABSEL/SINCERITIES

SINCERITIES is a tool for inferring gene regulatory networks from time-stamped cross-sectional single cell transcriptional expression profiles.

Size: 16.6 MB - Last synced at: about 2 months ago - Pushed at: over 7 years ago - Stars: 13 - Forks: 5

obophenotype/provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL

Language: Makefile - Size: 112 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 12 - Forks: 1

ocbe-uio/DIscBIO

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics

Language: Jupyter Notebook - Size: 230 MB - Last synced at: 7 days ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 5

sysbio-curie/transmorph

Computational framework for dataset integration

Language: Jupyter Notebook - Size: 199 MB - Last synced at: about 1 hour ago - Pushed at: almost 2 years ago - Stars: 11 - Forks: 2

gdurif/pCMF

pCMF R package

Language: C++ - Size: 271 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 11 - Forks: 0

cytomining/CytoTable

Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.

Language: Python - Size: 231 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 10 - Forks: 6

bioinfocz/scdrake

A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like pipeline toolkit for the R language.

Language: R - Size: 8.4 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 10 - Forks: 3

jhu99/vipcca

Single-cell alignment

Language: Python - Size: 9.9 MB - Last synced at: 13 days ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 3

CABSEL/CALISTA

CALISTA: Clustering And Lineage Inference in Single Cell Transcriptional Analysis

Language: HTML - Size: 102 MB - Last synced at: about 2 months ago - Pushed at: about 6 years ago - Stars: 9 - Forks: 2

pughlab/crescent

The CanceR Single Cell ExpressioN Toolkit one-line-command applications.

Language: R - Size: 4.8 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 8 - Forks: 4

gozsari/Single-Cell-Data-Analysis

Notes and studies about single-cell RNA-Seq analysis

Language: Python - Size: 9.45 MB - Last synced at: 17 days ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 4

rnabioco/raer

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

Language: C - Size: 22.3 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 8 - Forks: 2

Hon-lab/pySpade

Single cell Perturbations - Analysis of Differential gene Expression

Language: Python - Size: 1.46 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 8 - Forks: 0

satijalab/seurat-docker

Docker images of Seurat

Language: Dockerfile - Size: 117 KB - Last synced at: 26 days ago - Pushed at: 6 months ago - Stars: 8 - Forks: 8

lab-conrad/resVAE

resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.

Language: Jupyter Notebook - Size: 7.45 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 3

quadbio/scRNAseq_comparison_vignette

Tutorial of condition comparison analysis of scRNA-seq data

Size: 81.8 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 8 - Forks: 1

jumphone/scRef

A reference-based solution for single-cell analysis

Language: R - Size: 149 MB - Last synced at: 16 days ago - Pushed at: almost 5 years ago - Stars: 8 - Forks: 1

NIGMS/ATAC-Seq-and-Single-Cell-ATAC-Seq-Analysis

ATAC-seq and scATAC-seq module developed by the University of Nebraska Medical Center

Language: Jupyter Notebook - Size: 9.45 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 7 - Forks: 6

bdsc-tds/SPLIT

Profile purification of single-cell spatial transcriptomics data

Language: R - Size: 2.97 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 7 - Forks: 0

rraadd88/htsimaging

🔬Python package for high-throughput single-cell imaging analysis.

Language: Python - Size: 28.2 MB - Last synced at: 15 days ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 1

KorkinLab/DUSC

Deep Unsupervised Single-cell Clustering (DUSC) is a hybrid approach for cell type discovery in scRNA-seq data.

Language: Python - Size: 718 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 1

jst-seminar-rostlab-tum/genomics.ai

a web application to annotate and visualise single-cell sequencing data using neural networks

Language: JavaScript - Size: 269 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 3

kpatel427/multiome_analysis

Scripts for sincle cell multiome analysis

Language: R - Size: 37.1 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 1

LiuLab-Bioelectronics-Harvard/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 300 MB - Last synced at: 6 months ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 2

villani-lab/ircolitis

Analysis of single-cell RNA-seq data from patients with immunotherapy-related colitis.

Language: JavaScript - Size: 9.19 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 6 - Forks: 2

saeyslab/ViScore

Single-cell dimensionality reduction evaluation and benchmarking toolkit

Language: Python - Size: 8.01 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 6 - Forks: 0

multitalk/scCrossTalk

Infer and visualize cell-cell communication for single-cell RNA-seq data

Language: HTML - Size: 50.3 MB - Last synced at: 1 day ago - Pushed at: 5 months ago - Stars: 6 - Forks: 1

poseidonchan/scRNAkinetics

Biological prior guided RNA kinetics inference

Language: Jupyter Notebook - Size: 13.1 MB - Last synced at: 18 days ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 0

milescsmith/scRNAimputeR

A effort to collect all of the scRNA imputation methods and allow them to interface with scRNA-seq libraries (i. e. Seurat, SingleCellAssay, etc...)

Language: R - Size: 73.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0

shehio/Computational-Biology

Language: Jupyter Notebook - Size: 21.6 MB - Last synced at: 7 months ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 1

schwikowskilab/rNetSNE

Language: R - Size: 581 KB - Last synced at: about 1 year ago - Pushed at: almost 7 years ago - Stars: 6 - Forks: 3

SlavovLab/QuantQC

QuantQC is a package for quality control (QC) of single-cell proteomics data. It is optimized to work with nPOP, a method for massively parallel sample preparation on glass slides.

Language: HTML - Size: 34 MB - Last synced at: 33 minutes ago - Pushed at: about 1 hour ago - Stars: 5 - Forks: 2

rachelgriffard/optima

An open-source R package for the Tapestri platform for integrative single cell multiomics data analysis

Language: HTML - Size: 763 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 5 - Forks: 0

seankmartin/NeuroChaT Fork of mnislamraju/NeuroChaT

Analysis toolset with GUI for Neuroscience

Language: Python - Size: 6.99 MB - Last synced at: 15 days ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 5

michael-nakai/isopod

An R package to simulate and detect differential transcript usage in transcript-level single-cell datasets.

Language: R - Size: 596 KB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 4 - Forks: 0

kullrich/oggmap

oggmap is a python package to extract orthologous maps (short: orthomap or in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Oggmap results (gene ages per orthologous group) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

Language: Python - Size: 12.6 MB - Last synced at: 18 days ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 0