68 results found Sort:

satijalab
seurat satijalab
922
2.3k
other
76
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 7 months ago
scverse
scvi-tools scverse
365
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
4,123 commits to main branch, last one 4 days ago
COMBINE-lab
salmon COMBINE-lab
164
780
gpl-3.0
38
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
10x rnaseq salmon rna-seq sailfish scrna-seq c-plus-plus single-cell quasi-mapping transcriptome bioinformatics quantification gene-expression selective-alignment single-cell-rna-seq rna-seq-quantification
Created 2015-03-19
1,907 commits to master branch, last one 9 months ago
saeyslab
nichenetr saeyslab
119
499
unknown
14
NicheNet: predict active ligand-target links between interacting cells
rna-seq ligand-target gene-expression ligand-receptor data-integration network-inference single-cell-omics single-cell-rna-seq cell-cell-communication intercellular-communication
Created 2018-02-05
495 commits to master branch, last one 3 months ago
scverse
squidpy scverse
84
448
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
683 commits to main branch, last one 10 days ago
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
cole-trapnell-lab
monocle3 cole-trapnell-lab
103
355
other
21
This repository has no description...
single-cell-rna-seq
Created 2019-01-24
927 commits to master branch, last one 8 months ago
theislab
cellrank theislab
47
354
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
2,288 commits to main branch, last one 6 days ago
OmicsML
dance OmicsML
36
353
bsd-2-clause
7
DANCE: a deep learning library and benchmark platform for single-cell analysis
dance python benchmark single-cell data-science deep-learning multimodality bioinformatics machine-learning single-cell-rna-seq computational-biology graph-neural-networks spatial-transcriptomics single-cell-rna-sequencing
Created 2022-06-07
787 commits to main branch, last one 5 months ago
scRNA-tools
scRNA-tools scRNA-tools
77
309
mit
21
Table of software for the analysis of single-cell RNA-seq data.
tools rna-seq database software scrna-seq single-cell single-cell-rna-seq
Created 2016-09-09
3,643 commits to main branch, last one about a month ago
xuranw
MuSiC xuranw
100
240
gpl-3.0
5
Multi-subject Single Cell Deconvolution
single-cell-rna-seq statistical-genetics
Created 2018-04-08
147 commits to master branch, last one 9 months ago
samuel-marsh
scCustomize samuel-marsh
24
231
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
3,101 commits to master branch, last one 2 days ago
kharchenkolab
pagoda2 kharchenkolab
47
217
unknown
16
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
scrna-seq single-cell transcriptomics single-cell-rna-seq
Created 2017-04-25
1,483 commits to main branch, last one 9 months ago
kharchenkolab
conos kharchenkolab
39
202
gpl-3.0
12
R package for the joint analysis of multiple single-cell RNA-seq datasets
scrna-seq batch-correction single-cell-rna-seq
Created 2018-07-21
1,108 commits to main branch, last one 9 months ago
theislab
diffxpy theislab
23
193
bsd-3-clause
7
Differential expression analysis for single-cell RNA-seq data.
tensorflow bioinformatics transcriptomics gene-set-enrichment single-cell-rna-seq differential-expression
Created 2018-07-02
478 commits to master branch, last one about a year ago
dtm2451
dittoSeq dtm2451
18
191
mit
5
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
rna-seq color-blind single-cell visualization color-blindness single-cell-rna-seq
Created 2019-02-18
828 commits to devel branch, last one 7 months ago
saezlab
liana-py saezlab
22
175
gpl-3.0
3
LIANA+: an all-in-one framework for cell-cell communication
python spatial single-cell spatialomics ligand-receptor single-cell-rna-seq cell-cell-communication
Created 2022-09-22
810 commits to main branch, last one 3 months ago
COMBINE-lab
alevin-fry COMBINE-lab
15
174
bsd-3-clause
9
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
10x rust rna-seq single-cell quantification transcriptomics single-cell-rna-seq
Created 2020-07-15
827 commits to master branch, last one 14 days ago
kharchenkolab
numbat kharchenkolab
23
172
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
961 commits to main branch, last one 15 days ago
enblacar
SCpubr enblacar
13
164
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 4 months ago
quadbio
scRNAseq_analysis_vignette quadbio
58
163
unknown
7
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 8 months ago
stemangiola
tidyseurat stemangiola
12
159
unknown
9
Seurat meets tidyverse. The best of both worlds.
pca sct tsne umap dplyr purrr tidyr seurat tibble ggplot2 tidyverse single-cell transcripts normalization single-cell-rna-seq
Created 2020-08-23
414 commits to master branch, last one 5 months ago
pachterlab
kb_python pachterlab
23
157
bsd-2-clause
12
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
bustools kallisto kb-python scrna-seq single-cell-rna-seq rna-velocity-estimation
Created 2019-10-14
604 commits to master branch, last one 2 months ago
mojaveazure
seurat-disk mojaveazure
50
155
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
theislab
scCODA theislab
24
152
bsd-3-clause
9
A Bayesian model for compositional single-cell data analysis
tensorflow single-cell-rna-seq statistical-analysis compositional-changes
Created 2019-01-21
355 commits to master branch, last one about a year ago
pwwang
scplotter pwwang
16
133
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
42 commits to master branch, last one 10 days ago
saeyslab
multinichenetr saeyslab
14
128
gpl-3.0
3
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
scrna-seq single-cell ligand-target ligand-receptor systems-biology single-cell-rna-seq cell-cell-interaction cell-cell-communication differential-expression intercellular-signaling intercellular-communication ligand-receptor-interaction
Created 2021-02-16
135 commits to main branch, last one about a month ago
dynverse
dynmethods dynverse
26
121
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 about a year ago
hemberg-lab
SC3 hemberg-lab
55
121
gpl-3.0
11
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
human-cell-atlas single-cell-rna-seq bioconductor-package
Created 2016-01-28
363 commits to master branch, last one 5 years ago
martinjzhang
scDRS martinjzhang
16
117
mit
2
Single-cell disease relevance score (scDRS)
gwas cell-state single-cell-rna-seq diseases-and-complex-traits within-cell-type-heterogeneity
Created 2020-07-10
325 commits to master branch, last one 2 months ago