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single-cell-rna-seq

Here are 409 public repositories matching this topic...

satijalab / seurat

R toolkit for single cell genomics

cran single-cell-genomics single-cell-rna-seq human-cell-atlas

Updated Oct 25, 2024
R

scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse

Updated Nov 19, 2024
Python

COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

c-plus-plus bioinformatics rna-seq gene-expression rnaseq scrna-seq quantification transcriptome single-cell quasi-mapping salmon sailfish 10x single-cell-rna-seq selective-alignment rna-seq-quantification

Updated May 29, 2024
C++

saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells

rna-seq gene-expression network-inference data-integration single-cell-rna-seq single-cell-omics intercellular-communication ligand-receptor ligand-target cell-cell-communication

Updated Sep 5, 2024
R

squidpy

scverse / squidpy

Spatial Single Cell Analysis in Python

data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy

Updated Nov 18, 2024
Python

zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

scrna-seq shiny-apps single-cell shinyapps single-cell-genomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq seurat single-cell-omics scrna-seq-analysis single-cell-sequencing shiny-app scanpy scatac-seq anndata scrna-pipeline seurat-objects single-cell-pipeline

Updated May 21, 2024
R

OmicsML / dance

DANCE: a deep learning library and benchmark platform for single-cell analysis

python data-science benchmark machine-learning bioinformatics deep-learning computational-biology dance single-cell multimodality single-cell-rna-seq graph-neural-networks spatial-transcriptomics single-cell-rna-sequencing

Updated Nov 18, 2024
Python

cellrank

theislab / cellrank

CellRank: dynamics from multi-view single-cell data

data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning single-cell-genomics single-cell-rna-seq cell-fate-transitions fuzzy-clustering-analyses rna-velocity cell-fate-determination

Updated Oct 7, 2024
Python

cole-trapnell-lab / monocle3

single-cell-rna-seq

Updated Nov 9, 2024
R

scRNA-tools / scRNA-tools

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

rna-seq database tools software scrna-seq single-cell single-cell-rna-seq

Updated Nov 19, 2024
R

xuranw / MuSiC

Multi-subject Single Cell Deconvolution

statistical-genetics single-cell-rna-seq

Updated Mar 4, 2024
R

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.

visualization ggplot2 customization scrna-seq single-cell single-cell-genomics single-cell-rna-seq seurat

Updated Nov 15, 2024
R

kharchenkolab / pagoda2

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

scrna-seq transcriptomics single-cell single-cell-rna-seq

Updated Feb 27, 2024
JavaScript

kharchenkolab / conos

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

scrna-seq single-cell-rna-seq batch-correction

Updated Feb 26, 2024
R

theislab / diffxpy

Differential expression analysis for single-cell RNA-seq data.

bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq

Updated May 30, 2023
Python

dtm2451 / dittoSeq

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

visualization rna-seq color-blindness single-cell single-cell-rna-seq color-blind

Updated Sep 24, 2024
R

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.

rust rna-seq quantification transcriptomics single-cell 10x single-cell-rna-seq

Updated Nov 15, 2024
Rust

kharchenkolab / numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

cancer-genomics single-cell phylogeny single-cell-rna-seq single-cell-analysis cnv-detection spatial-transcriptomics lineage-tracing

Updated Sep 20, 2024
R

saezlab / liana-py

LIANA+: an all-in-one framework for cell-cell communication

python spatial single-cell single-cell-rna-seq ligand-receptor cell-cell-communication spatialomics

Updated Sep 21, 2024
Python

SCpubr

enblacar / SCpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.

visualization ggplot2 r data-visualization rstats single-cell single-cell-genomics single-cell-rna-seq publication-quality-plots seurat

Updated Aug 21, 2024
R

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