31 results found Sort:

sqjin
CellChat sqjin
145
640
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This repository has been archived (exclude archived)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
85
395
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
immunomind
immunarch immunomind
66
311
apache-2.0
14
🧬 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 8 months ago
r3fang
SnapATAC r3fang
126
306
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 2 years ago
satijalab
seurat-wrappers satijalab
131
305
gpl-3.0
11
Community-provided extensions to Seurat
community single-cell-analysis single-cell-genomics
Created 2019-04-24
359 commits to master branch, last one 7 months ago
jinworks
CellChat jinworks
50
292
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
109 commits to main branch, last one about a month ago
DingWB
PyComplexHeatmap DingWB
31
292
mit
6
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
469 commits to main branch, last one 2 days ago
slowkow
harmonypy slowkow
23
200
gpl-3.0
6
🎼 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 4 months ago
sunduanchen
Scissor sunduanchen
32
189
gpl-3.0
3
Scissor package
data-mining bioinformatics-tool single-cell-analysis
Created 2020-04-11
79 commits to master branch, last one 2 years ago
kharchenkolab
numbat kharchenkolab
23
168
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
958 commits to main branch, last one 2 months ago
quadbio
scRNAseq_analysis_vignette quadbio
58
155
unknown
6
Tutorial for scRNA-seq data analysis beginners using R
tutorial bioinformatics single-cell-rna-seq single-cell-analysis
Created 2020-04-19
37 commits to master branch, last one 7 months ago
dynverse
dynmethods dynverse
26
120
other
10
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 11 months ago
pwwang
scplotter pwwang
13
113
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
37 commits to master branch, last one 15 days ago
pinellolab
dictys pinellolab
14
111
agpl-3.0
3
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 4 months ago
GregorySchwartz
too-many-cells GregorySchwartz
19
105
gpl-3.0
3
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 23 days ago
yanwu2014
swne yanwu2014
19
104
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
JEFworks-Lab
HoneyBADGER JEFworks-Lab
31
97
gpl-3.0
8
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
singleron-RD
CeleScope singleron-RD
31
92
mit
3
Single Cell Analysis Pipelines
bioinformatics single-cell-analysis
Created 2020-07-29
1,789 commits to master branch, last one about a month ago
powellgenomicslab
Nebulosa powellgenomicslab
8
88
unknown
5
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 8 months ago
gao-lab
SLAT gao-lab
7
81
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
24 commits to main branch, last one 5 months ago
sankaranlab
SCAVENGE sankaranlab
34
80
gpl-3.0
4
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 about a year ago
labsyspharm
scimap labsyspharm
26
74
mit
3
Spatial Single-Cell Analysis Toolkit
pypi python image-analysis spatial-analysis single-cell-analysis
Created 2020-06-09
866 commits to master branch, last one a day ago
dynverse
dyngen dynverse
6
73
other
3
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
72
bsd-3-clause
6
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 about a year ago
poseidonchan
TAPE poseidonchan
9
48
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
quadbio
scMultiome_analysis_vignette quadbio
13
47
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 7 months ago
zjunlp
ChatCell zjunlp
9
46
other
8
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 9 months ago
wanglab-broad
ClusterMap wanglab-broad
11
41
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 4 months ago
berenslab
umi-normalization berenslab
2
41
agpl-3.0
8
Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology
scrna t-sne glm-pca umi-count normalization gene-selection umi-count-matrix negative-binomial single-cell-rna-seq single-cell-analysis negative-binomial-model dimensionality-reduction negative-binomial-regression
Created 2020-10-15
56 commits to main branch, last one 2 years ago
genecell
COSG genecell
6
38
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
21 commits to main branch, last one about a year ago