Ecosyste.ms: Repos

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

GitHub topics: scrna-seq

Repositories

interactivereport/cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

Language: HTML - Size: 119 MB - Last synced: 5 minutes ago - Pushed: about 1 hour ago - Stars: 121 - Forks: 42

dpeerlab/Palantir

Single cell trajectory detection

Language: Jupyter Notebook - Size: 55.7 MB - Last synced: about 17 hours ago - Pushed: 1 day ago - Stars: 195 - Forks: 45

OOAAHH/SRA_Analysis_WDL

用于bioos的大规模数据分析

Language: WDL - Size: 243 KB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 1 - Forks: 0

jamesjcai/scGEAToolbox

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Language: HTML - Size: 809 MB - Last synced: about 18 hours ago - Pushed: 2 days ago - Stars: 24 - Forks: 10

HaojiaWu/CellScopes.jl

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 126 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 17 - Forks: 2

pachterlab/kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

Language: Python - Size: 178 MB - Last synced: 2 days ago - Pushed: 4 months ago - Stars: 141 - Forks: 22

mdozmorov/scRNA-seq_notes

A list of scRNA-seq analysis tools

Language: R - Size: 1.17 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 548 - Forks: 135

chenyongrowan/scTIGER

The Single-cell Temporal Inference of Gene Regulatory (scTIGER) Networks method is a computational method designed to predict gene regulatory networks (GRNs) using paired datasets of case versus control experiments.

Language: Python - Size: 17.6 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

bnediction/scBoolSeq

scBoolSeq: scRNA-Seq data binarisation and synthetic generation from Boolean dynamics

Language: Python - Size: 195 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 4 - Forks: 0

saeyslab/multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Language: HTML - Size: 609 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 89 - Forks: 13

jiang-junyao/IReNA

R package IReNA

Language: R - Size: 131 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 25 - Forks: 12

ZJUFanLab/scDeepSort

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

Language: Python - Size: 19.4 MB - Last synced: 4 days ago - Pushed: 11 months ago - Stars: 93 - Forks: 17

mjoppich/cPred

Predict the celltype of a cluster from Seurat FindMarker data

Language: Python - Size: 1.01 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

zerostwo/scRNA_tutorial

scRNA-seq analysis pipeline.

Language: R - Size: 10.7 KB - Last synced: 5 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

obenno/StarScope

ThunderBio scRNA-seq pipeline

Language: Shell - Size: 84 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

aristoteleo/dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

Language: Python - Size: 7.18 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 404 - Forks: 58

liuzj039/jpy_tools

Language: Jupyter Notebook - Size: 270 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 7 - Forks: 0

AlexsLemonade/scpca-nf

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

Language: R - Size: 3.46 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 12 - Forks: 2

WT215/bayNormJL.jl

bayNorm in Julia.

Language: Julia - Size: 17.6 KB - Last synced: 7 days ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

mtvector/scANTIPODE

Variational Inference for Cell Type Evolution

Language: Python - Size: 5.12 GB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

nf-core/scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore

Language: Nextflow - Size: 20.8 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 5 - Forks: 3

igordot/clustermole

Unbiased single-cell transcriptomic data cell type identification

Language: R - Size: 17.8 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 11 - Forks: 0

theislab/zellkonverter

Conversion between scRNA-seq objects

Language: R - Size: 1.6 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 132 - Forks: 26

Zilong-Li/PCAone

Ultra-Fast Principal Component Analysis All in One

Language: C++ - Size: 4.81 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 27 - Forks: 2

scapeML/scape

Single-cell Analysis of Perturbational Effects using Machine Learning

Language: Python - Size: 3.1 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 3 - Forks: 2

Aavache/awesome-genetic-ai-papers

Recent awesome AI papers about genomics.

Size: 9.77 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

pathint/RankCompV3.jl

RankCompV3: a differential expression analysis algorithm based on the relative expression orderings (REOs) of gene pairs

Language: Julia - Size: 9.39 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 5 - Forks: 0

scverse/muon

muon is a multimodal omics Python framework

Language: Python - Size: 5.04 MB - Last synced: 5 days ago - Pushed: 16 days ago - Stars: 197 - Forks: 28

LieberInstitute/TREG

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Language: R - Size: 22.7 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 4 - Forks: 2

ankitbioinfo/nico_tutorial

A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and covariation patterns between interacted cell types.

Language: Jupyter Notebook - Size: 50.9 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 0 - Forks: 1

lilab-bcb/cirrocumulus

Bring your single-cell data to life

Language: JavaScript - Size: 223 MB - Last synced: 4 days ago - Pushed: 17 days ago - Stars: 64 - Forks: 10

Starlitnightly/scltnn

A composite regression neural network for latent timing prediction of single-cell RNA-seq data

Language: Jupyter Notebook - Size: 133 MB - Last synced: 13 days ago - Pushed: 9 months ago - Stars: 5 - Forks: 2

junjunlab/scRNAtoolVis

Useful functions to make your scRNA-seq plot more cool!

Language: R - Size: 22.7 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 224 - Forks: 22

potulabe/symphonypy

Port of symphony algorithm of single-cell reference atlas mapping to Python

Language: Jupyter Notebook - Size: 83.3 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 23 - Forks: 1

theislab/scgen

Single cell perturbation prediction

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

single-cell-genetics/vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference

Language: Python - Size: 4.25 MB - Last synced: 2 days ago - Pushed: 3 months ago - Stars: 66 - Forks: 23

eleozzr/desc

Deep Embedding for Single-cell Clustering

Language: Jupyter Notebook - Size: 168 MB - Last synced: 15 days ago - Pushed: about 1 month ago - Stars: 85 - Forks: 22

biobenkj/compartmap

Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq

Language: R - Size: 72.7 MB - Last synced: 21 days ago - Pushed: 8 months ago - Stars: 11 - Forks: 9

ocbe-uio/DIscBIO

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

Language: Jupyter Notebook - Size: 230 MB - Last synced: 7 days ago - Pushed: 6 months ago - Stars: 11 - Forks: 5

rezakj/iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

Language: R - Size: 68.2 MB - Last synced: 18 days ago - Pushed: about 2 months ago - Stars: 117 - Forks: 19

broadinstitute/Tangram

Spatial alignment of single cell transcriptomic data.

Language: Jupyter Notebook - Size: 141 MB - Last synced: 17 days ago - Pushed: 9 months ago - Stars: 220 - Forks: 45

ToryDeng/scCTS

scCTS: identifying the cell type specific marker genes from population-level single-cell RNA-seq

Language: R - Size: 11.8 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 0 - Forks: 0

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: 13 days ago - Pushed: about 2 months ago - Stars: 74 - Forks: 15

chengfgao/TopicVelo

TopicVelo: Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems

Language: Jupyter Notebook - Size: 8.09 MB - Last synced: 7 days ago - Pushed: 23 days ago - Stars: 12 - Forks: 2

theislab/scarches

Reference mapping for single-cell genomics

Language: Jupyter Notebook - Size: 784 MB - Last synced: 2 days ago - Pushed: about 1 month ago - Stars: 310 - Forks: 49

Oshlack/splatter

Simple simulation of single-cell RNA sequencing data

Language: R - Size: 57.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 205 - Forks: 55

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

Zhuang-Bio/scRNA_STseq_human_wounds_paper_scripts

Comprehensive analysis of single cell RNAseq and spatial transcriptomics in human acute and chronic wounds

Language: Jupyter Notebook - Size: 379 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0

Teichlab/celltypist

A tool for semi-automatic cell type classification

Language: Python - Size: 22 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 234 - Forks: 36

AlexUOM/Sinus-node-deconvolution

Code used for the deconvoluting right atrium and sinus node bulk RNA-Seq into scRNA-Seq

Language: Jupyter Notebook - Size: 398 KB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 0 - Forks: 0

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

chenyongrowan/DEGage

DEGage is a novel model-based method for gene differential expression analysis between two groups of scRNA-seq count data. It employs a novel family of discrete distributions for describing the difference of two NB distributions (named DOTNB).

Language: R - Size: 4.45 MB - Last synced: 24 days ago - Pushed: 25 days ago - Stars: 0 - Forks: 1

shiquan/PISA

A collection of tools to process single-cell omics datasets.

Language: C - Size: 6.37 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 35 - Forks: 8

kharchenkolab/pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

Language: JavaScript - Size: 78.4 MB - Last synced: 18 days ago - Pushed: 3 months ago - Stars: 191 - Forks: 47

kharchenkolab/conos

R package for the joint analysis of multiple single-cell RNA-seq datasets

Language: R - Size: 269 MB - Last synced: about 23 hours ago - Pushed: 3 months ago - Stars: 188 - Forks: 38

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

sanderlab/scPerturb

scPerturb: A resource and a python/R tool for single-cell perturbation data

Language: Jupyter Notebook - Size: 209 MB - Last synced: 20 days ago - Pushed: 4 months ago - Stars: 87 - Forks: 4

chanzuckerberg/cellxgene

An interactive explorer for single-cell transcriptomics data

Language: JavaScript - Size: 239 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 579 - Forks: 111

PMBio/MuDataSeurat

.h5mu files interface for Seurat

Language: R - Size: 3.98 MB - Last synced: 26 days ago - Pushed: 6 months ago - Stars: 20 - Forks: 7

Gartner-Lab/deMULTIplex2

deMULTIplex2: robust sample demultiplexing for scRNA-seq

Language: R - Size: 15.9 MB - Last synced: 13 days ago - Pushed: 7 months ago - Stars: 8 - Forks: 0

AntonioDeFalco/SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

Language: HTML - Size: 62.5 MB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 80 - Forks: 22

OceanGenomics/mudskipper

A tool for projecting genomic alignments to transcriptomic coordinates

Language: Rust - Size: 18.3 MB - Last synced: 12 days ago - Pushed: 9 months ago - Stars: 30 - Forks: 7

theislab/scPoli_legacy

scPoli legacy code for reproducibility

Language: Python - Size: 112 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

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

LamineTourelab/Tutorial

Tutorials on machine learning, artificial intelligence in general and in biomedical research.

Language: Jupyter Notebook - Size: 41.4 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 0

scRNA-tools/scRNA-tools

Table of software for the analysis of single-cell RNA-seq data.

Language: R - Size: 80.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 295 - Forks: 75

ethanmclark1/bioinformatics-sota-eval

Evaluating SOTA biologically-informed neural networks (KPNN, PGNN, and GNN) on scRNA-seq data for classification tasks

Language: Python - Size: 89.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

wheaton5/souporcell

Clustering scRNAseq by genotypes

Language: Python - Size: 1.63 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 147 - Forks: 41

hemberg-lab/scRNA.seq.course Fork of rstudio/bookdown-demo

Analysis of single cell RNA-seq data course

Language: TeX - Size: 365 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 665 - Forks: 359

Related Keywords

scrna-seq 355 single-cell 79 bioinformatics 64 scrna-seq-analysis 44 rna-seq 30 r 26 single-cell-rna-seq 26 transcriptomics 26 seurat 24 python 23 scatac-seq 22 visualization 18 machine-learning 15 genomics 14 single-cell-genomics 14 deep-learning 13 scanpy 12 clustering 12 scrnaseq 12 workflow 12 differential-expression 11 gene-expression 11 cite-seq 10 computational-biology 10 spatial-transcriptomics 10 single-cell-analysis 8 singlecell 8 snakemake 8 pipeline 8 scrna-seq-data 8 anndata 7 single-cell-omics 7 bioconductor 7 pseudotime 7 multi-omics 7 atac-seq 7 snrna-seq 7 10x 6 umap 6 human-cell-atlas 6 tsne 6 benchmarking 6 omics 5 integration 5 cell-type-classification 5 biomedical-data-science 5 multiomics 5 10x-genomics 5 bulk-rna-seq 5 scrna 5 covid-19 5 umi 5 classification 5 visium 5 pytorch 5 chip-seq 5 dimensionality-reduction 5 deconvolution 5 batch-effects 5 normalization 4 ngs 4 single-cell-atac-seq 4 seurat-objects 4 10xgenomics 4 marker-genes 4 eqtl 4 simulation 4 data-integration 4 database 4 imputation 4 pca 4 mudata 4 rare-disease 3 doublet-detection 3 transcription-factors 3 gwas 3 cell-fate-transitions 3 batch-correction 3 rna-velocity 3 dropout 3 svd 3 scslam-seq 3 vector-field 3 diffusion-maps 3 scrna-pipeline 3 cross-species 3 nextflow 3 rstats 3 variational-autoencoder 3 mapping 3 scrna-imputation-methods 3 deep-neural-networks 3 multimodal-omics 3 trajectory 3 dataviz 3 gene-regulatory-network 3 statistics 3 systems-biology 3 annotation 3 fastq 3

GitHub topics: scrna-seq

hemberg-lab/scRNA.seq.course Fork of rstudio/bookdown-demo

TomKellyGenetics/DoubletDetection Fork of JonathanShor/DoubletDetection

TomKellyGenetics/cellranger_clean Fork of mckinsel/cellranger_clean