12 results found Sort:

zhanghao-njmu
SCP zhanghao-njmu
88
407
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
liulab-dfci
MAESTRO liulab-dfci
78
278
gpl-3.0
12
Single-cell Transcriptome and Regulome Analysis Pipeline
scrna-seq scatac-seq epigenetics snakemake-workflows transcription-factors gene-regulatory-networks
Created 2019-07-16
614 commits to master branch, last one 3 years ago
scverse
muon scverse
31
222
bsd-3-clause
14
muon is a multimodal omics Python framework
muon mudata scanpy anndata scverse cite-seq scrna-seq scatac-seq multi-omics multimodal-data multimodal-omics-analysis
Created 2020-02-03
586 commits to main branch, last one about a month ago
pinellolab
STREAM pinellolab
48
173
agpl-3.0
16
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
python lineage scrna-seq scatac-seq singlecell trajectory visualization
Created 2018-04-12
471 commits to master branch, last one 3 years ago
sanderlab
scPerturb sanderlab
6
109
other
5
scPerturb: A resource and a python/R tool for single-cell perturbation data
r python science cite-seq database scrna-seq scatac-seq statistics single-cell perturbation
Created 2022-08-12
161 commits to master branch, last one 3 months ago
parashardhapola
scarf parashardhapola
12
98
bsd-3-clause
5
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
tsne umap big-data cite-seq genomics scrna-seq clustering multiomics pseudotime scatac-seq gene-modules bioinformatics graph-analytics memory-efficient dimension-reduction single-cell-rna-seq single-cell-atac-seq single-cell-genomics scalable-data-analysis differential-expression
Created 2020-05-07
1,024 commits to master branch, last one 4 days 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
alexisvdb
singleCellHaystack alexisvdb
9
79
other
5
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
r cite-seq pseudotime scatac-seq single-cell bioinformatics transcriptomics spatial-proteomics spatial-transcriptomics
Created 2019-02-13
446 commits to master branch, last one 11 months ago
genecell
COSGR genecell
9
54
bsd-3-clause
1
Accurate and fast cell marker gene identification with COSG
scrna-seq scatac-seq marker-genes spatial-transcriptomics
Created 2021-06-15
18 commits to main branch, last one about a year ago
swaruplabUCI
ArchRtoSignac swaruplabUCI
11
32
mit
0
An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
r scatac-seq
Created 2022-03-24
80 commits to main branch, last one 4 months ago
HaojiaWu
CellScopes.jl HaojiaWu
2
30
mit
4
A Julia package for single cell and spatial data analysis
visium xenium cartana merfish seqfish starmap data-viz slideseq scrna-seq scatac-seq julia-package bioinformatics single-cell-omics spatial-transcriptomics
Created 2022-12-26
1,005 commits to main branch, last one 3 months ago
aertslab
CREsted aertslab
2
28
other
7
CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
scverse scatac-seq deep-learning sequence-models regulatory-genomics single-cell-genomics
Created 2024-06-12
742 commits to main branch, last one 2 days ago