scrna-seq

There are 18 repositories under scrna-seq topic.

scverse / scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
scrna-seq variational-bayes variational-autoencoder cite-seq single-cell-genomics single-cell-rna-seq deep-generative-model human-cell-atlas scverse deep-learning
Language:Python 1157
COMBINE-lab / salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
quasi-mapping bioinformatics rna-seq rnaseq salmon quantification sailfish c-plus-plus gene-expression scrna-seq single-cell 10x selective-alignment rna-seq-quantification single-cell-rna-seq transcriptome
Language:C++ 746
hemberg-lab / scRNA.seq.course
Analysis of single cell RNA-seq data course
r scrna-seq scrna-seq-analysis bookdown sequencing course
Language:TeX 669
chanzuckerberg / cellxgene
An interactive explorer for single-cell transcriptomics data
scientific visualization scrna-seq transcriptomics dataviz
Language:JavaScript 593
scRNA-seq_notes
mdozmorov / scRNA-seq_notes
A list of scRNA-seq analysis tools
scrna-seq single-cell
Language:R 572
immunogenomics / harmony
Fast, sensitive and accurate integration of single-cell data with Harmony
algorithm data-integration r scrna-seq
Language:R 502
aristoteleo / dynamo-release
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
cell-fate differential-geometry dynamical-systems dynamo nasc-seq potential-landscape rna-acceleration rna-curvature rna-divergence rna-jacobian rna-velocity sci-fate scnt-seq scrna-seq scslam-seq vector-field
Language:Python 406
theislab / scarches
Reference mapping for single-cell genomics
single-cell deep-learning rna-seq-analysis data-integration batch-correction multimodal-deep-learning multiomics single-cell-genomics scrna-seq human-cell-atlas
Language:Jupyter Notebook 321
zhanghao-njmu / SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
single-cell seurat-objects single-cell-analysis single-cell-rna-seq scrna-pipeline scrna-seq scrna-seq-analysis seurat scanpy anndata single-cell-omics single-cell-sequencing shiny-apps shiny-app shinyapps single-cell-atac-seq single-cell-genomics single-cell-pipeline scatac-seq
Language:R 319
scRNA-tools / scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
database rna-seq scrna-seq single-cell single-cell-rna-seq software tools
Language:R 296
liulab-dfci / MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
epigenetics gene-regulatory-networks scatac-seq scrna-seq snakemake-workflows transcription-factors
Language:C 267
genecell / single-cell-papers-with-code
Papers with code for single cell related papers
single-cell scrna-seq scrna-seq-analysis reproducible-research reproducible-science single-cell-omics single-cell-atac-seq paper-with-code
260
theislab / scgen
Single cell perturbation prediction
transcriptomics deep-learning generative-model bioinformatics single-cell scrna-seq single-cell-genomics
Language:Python 252
Teichlab / celltypist
A tool for semi-automatic cell type classification
cell-type-classification label-transfer machine-learning python scrna-seq single-cell
Language:Python 250
scRNAtoolVis
junjunlab / scRNAtoolVis
Useful functions to make your scRNA-seq plot more cool!
elegant scrna-seq visualization yyds
Language:R 238
broadinstitute / Tangram
Spatial alignment of single cell transcriptomic data.
spatial-data visium gene-expression scrna-seq snrna-seq computational-biology
Language:Jupyter Notebook 231
splatter
Oshlack / splatter
Simple simulation of single-cell RNA sequencing data
bioconductor simulation scrna-seq bioinformatics
Language:R 210
dpeerlab / Palantir
Single cell trajectory detection
scrna-seq scrna-seq-analysis manifold-learning dimensionality-reduction diffusion-maps markov-chain differentiation single-cell-genomics trajectory-generation cell-fate-transitions
Language:Jupyter Notebook 202
scverse / muon
muon is a multimodal omics Python framework
multimodal-data multimodal-omics-analysis multi-omics anndata scanpy mudata muon scrna-seq scatac-seq cite-seq scverse
Language:Python 202
kharchenkolab / pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
single-cell transcriptomics scrna-seq single-cell-rna-seq
Language:JavaScript 195
kharchenkolab / conos
R package for the joint analysis of multiple single-cell RNA-seq datasets
scrna-seq single-cell-rna-seq batch-correction
Language:R 190
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.
customization ggplot2 seurat single-cell single-cell-genomics single-cell-rna-seq visualization scrna-seq
Language:R 181
pinellolab / STREAM
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
lineage python scatac-seq scrna-seq singlecell trajectory visualization
Language:Jupyter Notebook 168
wheaton5 / souporcell
Clustering scRNAseq by genotypes
scrna-seq scrnaseq scrna-seq-analysis bioinformatics computational-biology genomics
Language:Python 151
pachterlab / kb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
bustools kallisto single-cell-rna-seq rna-velocity-estimation scrna-seq kb-python
Language:Python 141
theislab / zellkonverter
Conversion between scRNA-seq objects
scrna-seq r conversion bioconductor
Language:R 133
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.
scrna-seq cellxgene scanpy visualization seurat svg publication-quality-plots cellxgene-vip
Language:HTML 124
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)).
singel-cell-sequencing clustering-algorithm clustering normalization umap pseudotime scrna-seq scvdj-seq cite-seq 3d intractive-graph 10xgenomics dropout batch-normalization imputation diffusion-maps cell-type-classification icellr
Language:R 119
ZJUFanLab / bulk2space
a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles
bulk-sequencing deep-learning scrna-seq spatial-transcriptomics
Language:Jupyter Notebook 100
saeyslab / multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
cell-cell-communication differential-expression intercellular-communication intercellular-signaling ligand-receptor ligand-receptor-interaction ligand-target scrna-seq single-cell single-cell-rna-seq systems-biology cell-cell-interaction
Language:HTML 96
immunogenomics / symphony
Efficient and precise single-cell reference atlas mapping with Symphony
r scrna-seq bioinfo mapping
Language:Jupyter Notebook 94
ZJUFanLab / scDeepSort
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
single-cell transcriptomics deep-learning graph-neural-network cell-type-classification reference-free annotation scrna-seq gnn
Language:Python 94
sanderlab / scPerturb
scPerturb: A resource and a python/R tool for single-cell perturbation data
cite-seq database perturbation scatac-seq science scrna-seq single-cell python r statistics
Language:Jupyter Notebook 92
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.
bioinformatics single-cell-genomics single-cell-rna-seq dimension-reduction clustering umap tsne big-data cite-seq single-cell-atac-seq memory-efficient scalable-data-analysis scrna-seq scatac-seq pseudotime multiomics gene-modules differential-expression graph-analytics genomics
Language:Python 90
changwn / scFEA
single cell Flux Estimation Analysis (scFEA) Try the below web server!
single-cell metabolism scrna-seq metabolic-modules
Language:Jupyter Notebook 89
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.
single-cell copy-number-variation copynumber subclonal-deconvolution subclone-identification clonal-evolution clonal-analysis microenvironment tumor-heterogeneity tumor-classification tumor-evolution scrna-seq-analysis scrna-pipeline scrna-seq aneuploidy
Language:HTML 86