scrna-seq

There are 17 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 1125
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++ 728
hemberg-lab / scRNA.seq.course
Analysis of single cell RNA-seq data course
r scrna-seq scrna-seq-analysis bookdown sequencing course
Language:TeX 665
chanzuckerberg / cellxgene
An interactive explorer for single-cell transcriptomics data
scientific visualization scrna-seq transcriptomics dataviz
Language:JavaScript 582
scRNA-seq_notes
mdozmorov / scRNA-seq_notes
A list of scRNA-seq analysis tools
scrna-seq single-cell
Language:R 541
immunogenomics / harmony
Fast, sensitive and accurate integration of single-cell data with Harmony
algorithm data-integration r scrna-seq
Language:R 490
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 402
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 310
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 300
scRNA-tools / scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
single-cell rna-seq scrna-seq single-cell-rna-seq tools database software
Language:R 295
liulab-dfci / MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
scatac-seq scrna-seq epigenetics snakemake-workflows transcription-factors gene-regulatory-networks
Language:C 261
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
255
theislab / scgen
Single cell perturbation prediction
transcriptomics deep-learning generative-model bioinformatics single-cell scrna-seq single-cell-genomics
Language:Python 245
Teichlab / celltypist
A tool for semi-automatic cell type classification
python single-cell machine-learning scrna-seq cell-type-classification label-transfer
Language:Python 235
scRNAtoolVis
junjunlab / scRNAtoolVis
Useful functions to make your scRNA-seq plot more cool!
scrna-seq visualization elegant yyds
Language:R 221
broadinstitute / Tangram
Spatial alignment of single cell transcriptomic data.
spatial-data visium gene-expression scrna-seq snrna-seq computational-biology
Language:Jupyter Notebook 220
splatter
Oshlack / splatter
Simple simulation of single-cell RNA sequencing data
bioconductor simulation scrna-seq bioinformatics
Language:R 207
scverse / muon
muon is a multimodal omics Python framework
anndata cite-seq mudata multi-omics multimodal-data multimodal-omics-analysis muon scanpy scatac-seq scrna-seq scverse
Language:Python 196
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 194
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 191
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 188
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 174
pinellolab / STREAM
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
singlecell trajectory lineage visualization scatac-seq scrna-seq python
Language:Jupyter Notebook 170
wheaton5 / souporcell
Clustering scRNAseq by genotypes
scrna-seq scrnaseq scrna-seq-analysis bioinformatics computational-biology genomics
Language:Python 147
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 140
theislab / zellkonverter
Conversion between scRNA-seq objects
scrna-seq r conversion bioconductor
Language:R 132
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.
cellxgene cellxgene-vip publication-quality-plots scanpy scrna-seq seurat svg visualization
Language:HTML 121
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 116
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 98
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 93
immunogenomics / symphony
Efficient and precise single-cell reference atlas mapping with Symphony
bioinfo mapping r scrna-seq
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 89
saeyslab / multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
cell-cell-communication cell-cell-interaction differential-expression intercellular-communication intercellular-signaling ligand-receptor ligand-receptor-interaction ligand-target scrna-seq single-cell single-cell-rna-seq systems-biology
Language:HTML 89
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 87
eleozzr / desc
Deep Embedding for Single-cell Clustering
desc batch-remove scrna-seq deep-learning clustering
Language:Jupyter Notebook 86
catavallejos / BASiCS
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
bayesian single-cell scrna-seq r rcpp rcpparmadillo gene-expression bioconductor-package
Language:R 83