single-cell-rna-seq

There are 33 repositories under single-cell-rna-seq topic.

satijalab / seurat
R toolkit for single cell genomics
human-cell-atlas single-cell-rna-seq single-cell-genomics cran
Language:R 2251
scverse / scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
cite-seq deep-generative-model deep-learning human-cell-atlas scrna-seq scverse single-cell-genomics single-cell-rna-seq variational-autoencoder variational-bayes
Language:Python 1207
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++ 771
saeyslab / nichenetr
NicheNet: predict active ligand-target links between interacting cells
cell-cell-communication data-integration gene-expression intercellular-communication ligand-receptor ligand-target network-inference rna-seq single-cell-omics single-cell-rna-seq
Language:R 467
squidpy
scverse / squidpy
Spatial Single Cell Analysis in Python
data-visualization image-analysis single-cell-genomics single-cell-rna-seq spatial-analysis spatial-transcriptomics squidpy
Language:Python 424
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 358
OmicsML / dance
DANCE: a deep learning library and benchmark platform for single-cell analysis
benchmark bioinformatics computational-biology dance data-science deep-learning graph-neural-networks machine-learning multimodality python single-cell single-cell-rna-seq single-cell-rna-sequencing spatial-transcriptomics
Language:Python 348
cellrank
theislab / cellrank
CellRank: dynamics from multi-view single-cell data
bioinformatics cell-fate-determination cell-fate-transitions data-science fuzzy-clustering-analyses genetics machine-learning manifold-learning markov-chains rna-velocity single-cell-genomics single-cell-rna-seq trajectory-generation
Language:Python 342
cole-trapnell-lab / monocle3
single-cell-rna-seq
Language:R 327
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 303
xuranw / MuSiC
Multi-subject Single Cell Deconvolution
single-cell-rna-seq statistical-genetics
Language:R 228
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 204
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 scrna-seq seurat single-cell single-cell-genomics single-cell-rna-seq visualization
Language:R 201
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 191
theislab / diffxpy
Differential expression analysis for single-cell RNA-seq data.
differential-expression single-cell-rna-seq gene-set-enrichment bioinformatics transcriptomics tensorflow
Language:Python 191
dtm2451 / dittoSeq
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
rna-seq single-cell single-cell-rna-seq visualization color-blindness color-blind
Language:R 185
COMBINE-lab / alevin-fry
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
single-cell rust transcriptomics rna-seq single-cell-rna-seq quantification 10x
Language:Rust 165
kharchenkolab / numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
cancer-genomics cnv-detection lineage-tracing phylogeny single-cell single-cell-analysis single-cell-rna-seq spatial-transcriptomics
Language:R 163
saezlab / liana-py
LIANA+: an all-in-one framework for cell-cell communication
cell-cell-communication ligand-receptor python single-cell single-cell-rna-seq spatial spatialomics
Language:Python 156
stemangiola / tidyseurat
Seurat meets tidyverse. The best of both worlds.
dplyr ggplot2 normalization pca purrr sct seurat single-cell single-cell-rna-seq tibble tidyr tidyverse transcripts tsne umap
Language:R 155
SCpubr
enblacar / SCpubr
Generate high quality, publication ready visualizations for single cell transcriptomics data.
data-visualization ggplot2 publication-quality-plots r rstats seurat single-cell-genomics single-cell-rna-seq visualization single-cell
Language:R 150
theislab / scCODA
A Bayesian model for compositional single-cell data analysis
tensorflow compositional-changes statistical-analysis single-cell-rna-seq
Language:Jupyter Notebook 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 145
mojaveazure / seurat-disk
Interfaces for HDF5-based Single Cell File Formats
single-cell-rna-seq single-cell-genomics hdf5-format
Language:R 142
quadbio / scRNAseq_analysis_vignette
Tutorial for scRNA-seq data analysis beginners using R
bioinformatics single-cell-analysis single-cell-rna-seq tutorial
137
hemberg-lab / SC3
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
bioconductor-package human-cell-atlas single-cell-rna-seq
Language:R 119
dynverse / dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
bioinformatics-algorithms pseudotemporal-ordering single-cell-analysis single-cell-rna-seq trajectory-inference trajectory-inference-methods
Language:R 118
tallulandrews / scRNASeqPipeline
rna-seq single-cell single-cell-rna-seq
Language:Perl 118
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 113
rnabioco / clustifyr
Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
rna-seq clusters marker-genes assign-identities single-cell-rna-seq
Language:R 109
martinjzhang / scDRS
Single-cell disease relevance score (scDRS)
cell-state gwas single-cell-rna-seq diseases-and-complex-traits within-cell-type-heterogeneity
Language:Jupyter Notebook 106
satijalab / azimuth
A Shiny web app for mapping datasets using Seurat v4
single-cell-rna-seq single-cell-genomics shiny-app
Language:HTML 106
tanaylab / metacell
Metacell - Single-cell mRNA Analysis
single-cell-rna-seq
Language:R 105
GregorySchwartz / too-many-cells
Cluster single cells and analyze cell clade relationships with colorful visualizations.
single-cell visualization single-cell-analysis single-cell-rna-seq bioinformatics-pipeline bioinformatics-algorithms
Language:Haskell 104
yanwu2014 / swne
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
single-cell-rna-seq single-cell-analysis data-visualization dimensionality-reduction nonnegative-matrix-factorization bioinformatics single-cell-genomics statistical-methods single-cell-atac-seq
Language:R 103
ttgump / scDeepCluster
scDeepCluster for Single Cell RNA-seq data
deep-learning single-cell-rna-seq unsupervised-learning
Language:Jupyter Notebook 99