single-cell-analysis

There are 9 repositories under single-cell-analysis topic.

sqjin / CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
cell-cell-communication single-cell-analysis cell-cell-interaction microenvironment
Language:R 584
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 296
r3fang / SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
single-cell-atac-seq single-cell-analysis bioinformatics-pipeline epigenetics machine-learning-algorithms sequencing
Language:R 295
immunomind / immunarch
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
immunology tcr tcr-repertoire immunoinformatics immune-repertoire rep-seq bcr-repertoire bcr ig ig-repertoire bioinformatics immune-repertoire-data immune-repertoire-analysis t-cell-receptor b-cell-receptor immunoglobulin repertoire-analysis airr-analysis single-cell single-cell-analysis
Language:R 286
satijalab / seurat-wrappers
Community-provided extensions to Seurat
community single-cell-analysis single-cell-genomics
Language:R 279
DingWB / PyComplexHeatmap
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
clustermap heatmap visualization matplotlib pandas plot python complexheatmap bioinformatics complex-heatmaps data-visualization-python single-cell-analysis
Language:Python 223
slowkow / harmonypy
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
data-science data-integration bioinformatics single-cell-analysis
Language:Python 172
sunduanchen / Scissor
Scissor package
bioinformatics-tool data-mining single-cell-analysis
Language:C++ 157
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 146
jinworks / CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
cell-cell-communication cell-cell-interaction microenvironment single-cell-analysis spatial-transcriptomics
Language:R 143
dynverse / dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
single-cell-rna-seq single-cell-analysis bioinformatics-algorithms trajectory-inference-methods trajectory-inference pseudotemporal-ordering
Language:R 113
quadbio / scRNAseq_analysis_vignette
Tutorial for scRNA-seq data analysis beginners using R
bioinformatics single-cell-analysis single-cell-rna-seq tutorial
105
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
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 99
pinellolab / dictys
Context specific and dynamic gene regulatory network reconstruction and analysis
dynamic-network gene-regulatory-network network-analysis network-inference network-visualization single-cell-analysis single-cell-multiomics single-cell-network
Language:Python 97
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 93
singleron-RD / CeleScope
Single Cell Analysis Pipelines
bioinformatics single-cell-analysis
Language:Python 76
sankaranlab / SCAVENGE
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
cell-heterogeneity cell-state cell-trajectory complex-traits disease-mechanisms fine-mapping network-propagation random-walk scatac-seq single-cell-analysis causal-celltype gwas-tool single-cell disease-celltype
Language:R 72
chriscainx / mnnpy
An implementation of MNN (Mutual Nearest Neighbors) correct in python.
biological-data-analysis bioinformatics-tool single-cell-analysis batch-effects mnn-correct mutual-nearest-neighbor
Language:Python 68
dynverse / dyngen
Simulating single-cell data using gene regulatory networks 📠
single-cell single-cell-analysis single-cell-omics benchmarking
Language:HTML 68
powellgenomicslab / Nebulosa
R package to visualize gene expression data based on weighted kernel density estimation
single-cell single-cell-analysis single-cell-multiomics single-cell-rna-seq
Language:R 63
SLAT
gao-lab / SLAT
Spatial-Linked Alignment Tool
bioinformatics single-cell spatial-data spatial-transcriptomics single-cell-analysis deep-learning graph-neural-networks
Language:Python 58
labsyspharm / scimap
Spatial Single-Cell Analysis Toolkit
image-analysis python single-cell-analysis spatial-analysis pypi
Language:Python 54
poseidonchan / TAPE
Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)
deep-learning machine-learning single-cell-analysis computational-biology cell-composition-analysis bioinformatics rna-seq precision-medicine cell-type-specific-gene-expression-analysis
Language:Jupyter Notebook 41
theislab / pseudodynamics
Dynamic models for single-cell RNA-seq time series.
single-cell-analysis time-series single-cell-rna-seq population-dynamics
Language:Jupyter Notebook 39
berenslab / umi-normalization
Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology
scrna single-cell-rna-seq single-cell-analysis umi-count umi-count-matrix normalization glm-pca negative-binomial-regression negative-binomial-model negative-binomial t-sne dimensionality-reduction gene-selection
Language:Jupyter Notebook 37
wanglab-broad / ClusterMap
ClusterMap for multi-scale clustering analysis of spatial gene expression
in-situ-sequencing spatial-transcriptomics single-cell-analysis spatial-omics bioinformatics cell-segmentation transcriptomics
Language:Jupyter Notebook 37
RabadanLab / randomly
A Library for Denoising Single-Cell Data with Random Matrix Theory
single-cell data-analysis random-matrix-theory sparsity denoising dropout single-cell-omics single-cell-rna-seq single-cell-analysis
Language:Jupyter Notebook 36
genecell / COSG
Accurate and fast cell marker gene identification with COSG
single-cell single-cell-rna-seq single-cell-analysis single-cell-atac-seq spatial-transcriptomics
Language:Jupyter Notebook 35
nasqar / seuratv3wizard
A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
seurat r shiny shiny-apps single-cell single-cell-rna-seq single-cell-analysis single-cell-genomics webapp visualization bioinformatics
Language:R 32
zjunlp / ChatCell
ChatCell: Facilitating Single-Cell Analysis with Natural Language
ai4science artificial-intelligence bioinformatics biology cell chatcell interdisciplinary large-language-models natural-language-processing pre-trained-language-models single-cell single-cell-analysis llm4bio
Language:Python 32
ciccalab / SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
cell-segmentation single-cell-analysis imaging-mass-cytometry immunofluorescence histological-images gating tissue-analysis tissue-classification histology bioimage-analysis bioimaging bioimage-tools bioimage-informatics mcd imc life-sciences-image ome-tiff image-analysis-workflows
Language:R 31
KChen-lab / bindSC
Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data
integrative-analysis single-cell-analysis
Language:R 30
YangLabHKUST / Portal
Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets
single-cell-analysis data-integration deep-learning
Language:Python 30
SGI-LungCancer / SingleCell
Code repository for single cell RNA-seq
single-cell-analysis single-cell-rna-seq
Language:R 29
xzhoulab / DRComparison
Comparison of dimensionality reduction methods
single-cell-analysis dimensionality-reduction
Language:R 29