25 results found Sort:

satijalab
seurat satijalab
918
2.3k
other
74
R toolkit for single cell genomics
cran human-cell-atlas single-cell-rna-seq single-cell-genomics
Created 2015-05-20
8,541 commits to master branch, last one 6 months ago
scverse
scvi-tools scverse
355
1.3k
bsd-3-clause
26
Deep probabilistic analysis of single-cell and spatial omics data
scverse cite-seq scrna-seq deep-learning human-cell-atlas variational-bayes single-cell-rna-seq single-cell-genomics deep-generative-model variational-autoencoder
Created 2017-09-06
4,101 commits to main branch, last one 2 days ago
scverse
squidpy scverse
82
440
bsd-3-clause
10
Spatial Single Cell Analysis in Python
squidpy image-analysis spatial-analysis data-visualization single-cell-rna-seq single-cell-genomics spatial-transcriptomics
Created 2020-08-21
678 commits to main branch, last one 10 days ago
zhanghao-njmu
SCP zhanghao-njmu
87
397
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
theislab
cellrank theislab
46
350
bsd-3-clause
8
CellRank: dynamics from multi-view single-cell data
genetics data-science rna-velocity markov-chains bioinformatics machine-learning manifold-learning single-cell-rna-seq single-cell-genomics cell-fate-transitions trajectory-generation cell-fate-determination fuzzy-clustering-analyses
Created 2020-03-12
2,287 commits to main branch, last one about a month ago
theislab
scarches theislab
51
335
bsd-3-clause
12
Reference mapping for single-cell genomics
scrna-seq multiomics single-cell deep-learning batch-correction data-integration human-cell-atlas rna-seq-analysis single-cell-genomics multimodal-deep-learning
Created 2019-08-12
1,175 commits to master branch, last one 5 months ago
satijalab
seurat-wrappers satijalab
131
306
gpl-3.0
11
Community-provided extensions to Seurat
community single-cell-analysis single-cell-genomics
Created 2019-04-24
391 commits to master branch, last one 12 hours ago
theislab
scgen theislab
56
268
gpl-3.0
9
Single cell perturbation prediction
scrna-seq single-cell deep-learning bioinformatics transcriptomics generative-model single-cell-genomics
Created 2018-11-28
422 commits to master branch, last one about a year ago
kaizhang
SnapATAC2 kaizhang
26
231
unknown
9
Single-cell epigenomics analysis tools
single-cell-genomics
Created 2021-12-04
470 commits to main branch, last one 2 days ago
dpeerlab
Palantir dpeerlab
52
224
gpl-2.0
11
Single cell trajectory detection
scrna-seq markov-chain diffusion-maps differentiation manifold-learning scrna-seq-analysis single-cell-genomics cell-fate-transitions trajectory-generation dimensionality-reduction
Created 2017-11-22
273 commits to master branch, last one 3 days ago
samuel-marsh
scCustomize samuel-marsh
24
219
gpl-3.0
3
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
seurat ggplot2 scrna-seq single-cell customization visualization single-cell-rna-seq single-cell-genomics
Created 2021-09-29
2,374 commits to master branch, last one 8 months ago
enblacar
SCpubr enblacar
13
158
gpl-3.0
6
Generate high quality, publication ready visualizations for single cell transcriptomics data.
r rstats seurat ggplot2 single-cell visualization data-visualization single-cell-rna-seq single-cell-genomics publication-quality-plots
Created 2021-12-21
734 commits to main branch, last one 3 months ago
mojaveazure
seurat-disk mojaveazure
49
152
gpl-3.0
14
Interfaces for HDF5-based Single Cell File Formats
hdf5-format single-cell-rna-seq single-cell-genomics
Created 2019-12-16
176 commits to master branch, last one about a year ago
satijalab
seurat-data satijalab
47
129
gpl-3.0
9
Dataset distribution for Seurat
datasets single-cell single-cell-genomics
Created 2019-05-29
97 commits to master branch, last one about a year ago
satijalab
azimuth satijalab
32
112
gpl-3.0
9
A Shiny web app for mapping datasets using Seurat v4
shiny-app single-cell-rna-seq single-cell-genomics
Created 2020-09-16
873 commits to master branch, last one about a year 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
10XGenomics
loupeR 10XGenomics
15
100
other
10
Convert Seurat objects to 10x Genomics Loupe files.
r-package 10xgenomics single-cell-genomics
Created 2023-08-23
28 commits to main branch, last one 24 days 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
1,018 commits to master branch, last one about a month ago
theislab
cpa theislab
17
88
bsd-3-clause
5
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs...
scrna-seq human-cell-atlas single-cell-rna-seq single-cell-genomics
Created 2021-10-15
344 commits to main branch, last one 3 months ago
jsxlei
SCALEX jsxlei
18
73
bsd-3-clause
4
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
scalex single-cell deep-learning online-integration single-cell-genomics
Created 2021-03-09
92 commits to main branch, last one 8 hours ago
calico
scnym calico
12
73
apache-2.0
6
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
rna-seq single-cell semi-supervised adversarial-training single-cell-genomics
Created 2019-07-29
34 commits to master branch, last one 11 months ago
GuangyuWangLab2021
cellDancer GuangyuWangLab2021
10
64
bsd-3-clause
0
Predict RNA velocity through deep learning
cell-fate rna-splicing rna-velocity transcriptomics single-cell-rna-seq single-cell-genomics rna-splicing-analysis rna-velocity-estimation
Created 2023-01-23
583 commits to main branch, last one 11 months ago
broadinstitute
single_cell_portal_core broadinstitute
26
63
bsd-3-clause
17
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
human-cell-atlas rna-seq-analysis single-cell-genomics
Created 2016-03-17
12,487 commits to development branch, last one 7 days ago
LiQian-XC
sctour LiQian-XC
4
52
mit
3
A deep learning architecture for robust inference and accurate prediction of cellular dynamics
pseudotime latent-space vector-field deep-learning single-cell-genomics inference-and-prediction
Created 2022-01-03
94 commits to main branch, last one about a year ago
pinellolab
pyrovelocity pinellolab
5
43
agpl-3.0
8
𝒫robabilistic modeling of RNA velocity ⬱
pyro multiomics rna-splicing rna-velocity transcriptomics single-cell-rna-seq probabilistic-models single-cell-genomics deep-generative-model rna-splicing-analysis single-cell-multiomics cell-fate-determination rna-velocity-estimation probabilistic-programming developmental-trajectories
Created 2022-09-07
1,947 commits to main branch, last one 3 months ago