34 results found Sort:

sqjin
CellChat sqjin
156
679
gpl-3.0
14
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
microenvironment single-cell-analysis cell-cell-interaction cell-cell-communication
This repository has been archived (exclude archived)
Created 2020-04-27
270 commits to master branch, last one about a year ago
zhanghao-njmu
SCP zhanghao-njmu
100
464
gpl-3.0
8
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
scanpy seurat anndata scrna-seq shiny-app shinyapps scatac-seq shiny-apps single-cell scrna-pipeline seurat-objects single-cell-omics scrna-seq-analysis single-cell-rna-seq single-cell-analysis single-cell-atac-seq single-cell-genomics single-cell-pipeline single-cell-sequencing
Created 2022-03-30
308 commits to main branch, last one about a year ago
jinworks
CellChat jinworks
61
367
gpl-3.0
2
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
microenvironment single-cell-analysis cell-cell-interaction cell-cell-communication spatial-transcriptomics
Created 2023-11-05
112 commits to main branch, last one 3 months ago
satijalab
seurat-wrappers satijalab
135
325
gpl-3.0
10
Community-provided extensions to Seurat
community single-cell-analysis single-cell-genomics
Created 2019-04-24
391 commits to master branch, last one 4 months ago
immunomind
immunarch immunomind
68
317
apache-2.0
13
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
ig bcr tcr rep-seq immunology single-cell airr-analysis ig-repertoire bcr-repertoire bioinformatics immunoglobulin tcr-repertoire b-cell-receptor t-cell-receptor immune-repertoire immunoinformatics repertoire-analysis single-cell-analysis immune-repertoire-data immune-repertoire-analysis
Created 2019-02-26
683 commits to master branch, last one about a year ago
r3fang
SnapATAC r3fang
130
314
gpl-3.0
14
Analysis Pipeline for Single Cell ATAC-seq
sequencing epigenetics single-cell-analysis single-cell-atac-seq bioinformatics-pipeline machine-learning-algorithms
Created 2019-02-19
228 commits to master branch, last one 3 years ago
DingWB
PyComplexHeatmap DingWB
34
314
mit
5
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
plot pandas python heatmap clustermap matplotlib visualization bioinformatics complexheatmap complex-heatmaps single-cell-analysis data-visualization-python
Created 2022-05-05
479 commits to main branch, last one 2 months ago
slowkow
harmonypy slowkow
22
217
gpl-3.0
5
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
data-science bioinformatics data-integration single-cell-analysis
Created 2019-12-19
72 commits to master branch, last one 8 months ago
sunduanchen
Scissor sunduanchen
35
211
gpl-3.0
3
Scissor package
data-mining bioinformatics-tool single-cell-analysis
Created 2020-04-11
79 commits to master branch, last one 3 years ago
quadbio
scRNAseq_analysis_vignette quadbio
63
183
unknown
7
Tutorial for scRNA-seq data analysis beginners using R
tutorial bioinformatics single-cell-rna-seq single-cell-analysis
Created 2020-04-19
38 commits to master branch, last one 18 days ago
kharchenkolab
numbat kharchenkolab
23
180
other
9
Haplotype-aware CNV analysis from single-cell RNA-seq
phylogeny single-cell cnv-detection cancer-genomics lineage-tracing single-cell-rna-seq single-cell-analysis spatial-transcriptomics
Created 2021-05-25
964 commits to main branch, last one 4 days ago
pwwang
scplotter pwwang
17
142
gpl-3.0
1
scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.
visualization single-cell-rna-seq single-cell-analysis single-cell-sequencing
Created 2024-09-03
58 commits to master branch, last one 4 days ago
dynverse
dynmethods dynverse
26
126
other
9
A collection of 50+ trajectory inference methods within a common interface 📥📤
single-cell-rna-seq single-cell-analysis trajectory-inference pseudotemporal-ordering bioinformatics-algorithms trajectory-inference-methods
Created 2017-11-14
1,315 commits to master branch, last one about a year ago
pinellolab
dictys pinellolab
13
114
agpl-3.0
5
Context specific and dynamic gene regulatory network reconstruction and analysis
dynamic-network network-analysis network-inference single-cell-network single-cell-analysis network-visualization single-cell-multiomics gene-regulatory-network
Created 2022-07-01
91 commits to master branch, last one 8 months ago
GregorySchwartz
too-many-cells GregorySchwartz
18
106
gpl-3.0
2
Cluster single cells and analyze cell clade relationships with colorful visualizations.
single-cell visualization single-cell-rna-seq single-cell-analysis bioinformatics-pipeline bioinformatics-algorithms
Created 2019-01-10
395 commits to master branch, last one 4 months ago
yanwu2014
swne yanwu2014
19
105
bsd-3-clause
5
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
bioinformatics data-visualization single-cell-rna-seq statistical-methods single-cell-analysis single-cell-atac-seq single-cell-genomics dimensionality-reduction nonnegative-matrix-factorization
Created 2018-01-03
270 commits to master branch, last one about a year ago
powellgenomicslab
Nebulosa powellgenomicslab
10
99
unknown
3
R package to visualize gene expression data based on weighted kernel density estimation
single-cell single-cell-rna-seq single-cell-analysis single-cell-multiomics
Created 2020-07-12
120 commits to master branch, last one about a year ago
singleron-RD
CeleScope singleron-RD
34
97
mit
2
Single Cell Analysis Pipelines
bioinformatics single-cell-analysis
Created 2020-07-29
1,842 commits to master branch, last one 3 days ago
JEFworks-Lab
HoneyBADGER JEFworks-Lab
31
96
gpl-3.0
7
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
hmm bayesian cnv-detection heterogeneity subpopulation bioinformatics transcriptomics single-cell-rna-seq single-cell-analysis
Created 2017-02-24
106 commits to master branch, last one 3 years ago
labsyspharm
scimap labsyspharm
29
86
mit
2
Spatial Single-Cell Analysis Toolkit
pypi python image-analysis spatial-analysis single-cell-analysis
Created 2020-06-09
890 commits to master branch, last one about a month ago
gao-lab
SLAT gao-lab
9
84
mit
2
Spatial-Linked Alignment Tool
single-cell spatial-data deep-learning bioinformatics single-cell-analysis graph-neural-networks spatial-transcriptomics
Created 2022-10-25
27 commits to main branch, last one 3 months ago
sankaranlab
SCAVENGE sankaranlab
34
83
gpl-3.0
3
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
gwas-tool cell-state scatac-seq random-walk single-cell fine-mapping complex-traits causal-celltype cell-trajectory disease-celltype cell-heterogeneity disease-mechanisms network-propagation single-cell-analysis
Created 2022-01-09
40 commits to main branch, last one 2 years ago
dynverse
dyngen dynverse
6
74
other
2
Simulating single-cell data using gene regulatory networks 📠
single-cell benchmarking single-cell-omics single-cell-analysis
Created 2017-03-10
1,169 commits to master branch, last one 2 years ago
chriscainx
mnnpy chriscainx
32
73
bsd-3-clause
5
An implementation of MNN (Mutual Nearest Neighbors) correct in python.
mnn-correct batch-effects bioinformatics-tool single-cell-analysis mutual-nearest-neighbor biological-data-analysis
Created 2018-04-19
100 commits to master branch, last one 2 years ago
quadbio
scMultiome_analysis_vignette quadbio
14
54
unknown
2
Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
tutorial bioinformatics single-cell-rna-seq single-cell-analysis single-cell-atac-seq single-cell-multiomics
Created 2022-04-24
11 commits to main branch, last one 11 months ago
poseidonchan
TAPE poseidonchan
11
53
gpl-3.0
3
Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)
rna-seq deep-learning bioinformatics machine-learning precision-medicine single-cell-analysis computational-biology cell-composition-analysis cell-type-specific-gene-expression-analysis
Created 2021-07-15
108 commits to main branch, last one about a year ago
EliHei2
segger_dev EliHei2
5
52
mit
2
a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imagin...
ai graphs xenium oncology segmentation spatial-omics molecule-graphs cell-segmentation single-cell-analysis graph-neural-networks spatial-transcriptomics
Created 2024-08-05
389 commits to main branch, last one 11 days ago
zjunlp
ChatCell zjunlp
10
48
other
6
ChatCell: Facilitating Single-Cell Analysis with Natural Language
cell biology llm4bio chatcell ai4science single-cell bioinformatics interdisciplinary single-cell-analysis large-language-models artificial-intelligence natural-language-processing pre-trained-language-models
Created 2023-12-19
170 commits to main branch, last one about a year ago
wanglab-broad
ClusterMap wanglab-broad
11
45
gpl-3.0
1
ClusterMap for multi-scale clustering analysis of spatial gene expression
spatial-omics bioinformatics transcriptomics cell-segmentation in-situ-sequencing single-cell-analysis spatial-transcriptomics
Created 2021-09-29
76 commits to main branch, last one 8 months ago
genecell
COSG genecell
8
43
bsd-3-clause
1
Accurate and fast cell marker gene identification with COSG
single-cell single-cell-rna-seq single-cell-analysis single-cell-atac-seq spatial-transcriptomics
Created 2021-04-13
67 commits to main branch, last one 2 days ago