single-cell-rna-seq

There are 29 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 2127
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 1133
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++ 732
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 437
squidpy
scverse / squidpy
Spatial Single Cell Analysis in Python
single-cell-rna-seq single-cell-genomics spatial-transcriptomics spatial-analysis image-analysis data-visualization squidpy
Language:Python 391
OmicsML / dance
DANCE: a deep learning library and benchmark platform for single-cell analysis
bioinformatics dance data-science deep-learning graph-neural-networks machine-learning multimodality python single-cell spatial-transcriptomics benchmark computational-biology single-cell-rna-seq single-cell-rna-sequencing
Language:Python 323
cole-trapnell-lab / monocle3
single-cell-rna-seq
Language:R 312
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 305
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 301
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
xuranw / MuSiC
Multi-subject Single Cell Deconvolution
single-cell-rna-seq statistical-genetics
Language:R 213
kharchenkolab / pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
scrna-seq single-cell single-cell-rna-seq transcriptomics
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
theislab / diffxpy
Differential expression analysis for single-cell RNA-seq data.
bioinformatics differential-expression gene-set-enrichment single-cell-rna-seq tensorflow transcriptomics
Language:Python 174
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 173
dtm2451 / dittoSeq
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
color-blind color-blindness rna-seq single-cell single-cell-rna-seq visualization
Language:R 167
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.
10x quantification rna-seq rust single-cell single-cell-rna-seq transcriptomics
Language:Rust 152
kharchenkolab / numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
cancer-genomics cnv-detection single-cell phylogeny single-cell-analysis single-cell-rna-seq spatial-transcriptomics lineage-tracing
Language:R 151
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 143
pachterlab / kb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
bustools kallisto kb-python rna-velocity-estimation scrna-seq single-cell-rna-seq
Language:Python 141
mojaveazure / seurat-disk
Interfaces for HDF5-based Single Cell File Formats
single-cell-rna-seq single-cell-genomics hdf5-format
Language:R 134
theislab / scCODA
A Bayesian model for compositional single-cell data analysis
tensorflow compositional-changes statistical-analysis single-cell-rna-seq
Language:Jupyter Notebook 134
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 single-cell-genomics single-cell-rna-seq visualization
Language:R 130
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 117
tallulandrews / scRNASeqPipeline
single-cell-rna-seq single-cell rna-seq
Language:Perl 117
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 115
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 114
quadbio / scRNAseq_analysis_vignette
Tutorial for scRNA-seq data analysis beginners using R
bioinformatics single-cell-analysis single-cell-rna-seq tutorial
108
tanaylab / metacell
Metacell - Single-cell mRNA Analysis
single-cell-rna-seq
Language:R 102
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 102
rnabioco / clustifyr
Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
assign-identities clusters marker-genes rna-seq single-cell-rna-seq
Language:R 101
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 100
ttgump / scDeepCluster
scDeepCluster for Single Cell RNA-seq data
single-cell-rna-seq deep-learning unsupervised-learning
Language:Jupyter Notebook 96
satijalab / azimuth
A Shiny web app for mapping datasets using Seurat v4
single-cell-rna-seq single-cell-genomics shiny-app
Language:HTML 95
JEFworks-Lab / HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
single-cell-analysis single-cell-rna-seq cnv-detection transcriptomics subpopulation hmm bayesian heterogeneity bioinformatics
Language:R 94
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 93