143 results found Sort:

seandavi
awesome-single-cell seandavi
988
3.2k
mit
248
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
python analysis atac-seq cell-cycle clustering single-cell awesome-list rna-seq-data cell-clusters bioinformatics scrna-seq-data gene-expression cell-populations data-integration analysis-pipeline data-visualization rna-seq-experiments cell-differentiation dimensionality-reduction gene-expression-profiles
Created 2016-06-29
791 commits to master branch, last one 6 days ago
bowang-lab
scGPT bowang-lab
205
1.0k
mit
33
This repository has no description...
gpt single-cell foundation-model
Created 2023-04-23
169 commits to main branch, last one 5 months ago
theislab
single-cell-best-practices theislab
185
780
other
19
https://www.sc-best-practices.org
book rna-seq tutorial single-cell
Created 2021-08-13
643 commits to master branch, last one 16 days ago
COMBINE-lab
salmon COMBINE-lab
165
777
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 8 months ago
mdozmorov
scRNA-seq_notes mdozmorov
146
635
mit
29
A list of scRNA-seq analysis tools
scrna-seq single-cell
Created 2018-08-30
478 commits to master branch, last one 2 days ago
flowhub-team
awesome-omics flowhub-team
66
549
mit
35
A collection of awesome things regarding all omics.
ngs omics awesome protein genomics single-cell ngs-pipeline wgs-analysis
Created 2022-02-15
216 commits to main branch, last one 10 months ago
KrishnaswamyLab
PHATE KrishnaswamyLab
75
475
other
18
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
single-cell manifold-learning data-visualization unsupervised-learning dimensionality-reduction
Created 2017-04-05
730 commits to main branch, last one about a month ago
Starlitnightly
omicverse Starlitnightly
57
471
gpl-3.0
6
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
omics single-cell bulk-rna-seq bioinformatics
Created 2021-03-22
436 commits to master branch, last one 7 days ago
aertslab
pySCENIC aertslab
183
444
gpl-3.0
18
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regula...
single-cell transcriptomics transcription-factors gene-regulatory-network
Created 2018-03-07
670 commits to master branch, last one 7 months ago
agitter
single-cell-pseudotime agitter
62
407
cc-by-4.0
33
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
rna-seq single-cell bioinformatics pseudotime-algorithms
Created 2016-06-25
267 commits to master branch, last one 22 days 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
welch-lab
liger welch-lab
78
390
gpl-3.0
22
R package for integrating and analyzing multiple single-cell datasets
r single-cell nonnegative-matrix-factorization
Created 2018-04-10
918 commits to master branch, last one 7 days ago
gao-lab
GLUE gao-lab
56
384
mit
8
Graph-linked unified embedding for single-cell multi-omics data integration
single-cell deep-learning bioinformatics single-cell-multiomics
Created 2021-08-22
35 commits to master branch, last one about a year ago
smorabit
hdWGCNA smorabit
35
360
other
5
High dimensional weighted gene co-expression network analysis
single-cell network-analysis gene-regulatory-network spatial-transcriptomics
Created 2020-08-11
234 commits to dev branch, last one 29 days ago
OmicsML
dance OmicsML
36
351
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 4 months ago
milaboratory
mixcr milaboratory
79
335
other
31
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
10x t-cell rep-seq rna-seq antibody immunology sequencing single-cell bioinformatics t-cell-receptor
Created 2015-03-30
3,986 commits to develop branch, last one 20 days 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
stuart-lab
signac stuart-lab
88
329
other
6
R toolkit for the analysis of single-cell chromatin data
atac single-cell bioinformatics
Created 2019-05-09
2,084 commits to master branch, last one 3 months 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
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
3,631 commits to main branch, last one 22 days ago
luntergroup
octopus luntergroup
38
305
mit
19
Bayesian haplotype-based mutation calling
phasing genomics variants haplotypes single-cell bioinformatics variant-calling de-novo-mutation somatic-variants
Created 2015-02-04
5,045 commits to develop branch, last one about a year ago
Teichlab
celltypist Teichlab
46
300
mit
8
A tool for semi-automatic cell type classification
python scrna-seq single-cell label-transfer machine-learning cell-type-classification
Created 2021-05-19
742 commits to main branch, last one 5 months ago
kpatel427
YouTubeTutorials kpatel427
130
291
mit
10
This repository has no description...
rna-seq youtube tutorials single-cell bioinformatics bioinformatics-analysis
Created 2021-11-29
119 commits to main branch, last one about a month ago
sdparekh
zUMIs sdparekh
67
275
gpl-3.0
13
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
dge umi fastq rnaseq rna-seq barcodes pipeline expression single-cell
Created 2017-06-20
291 commits to main branch, last one about a year ago
genecell
single-cell-papers-with-code genecell
70
272
unknown
12
Papers with code for single cell related papers
scrna-seq single-cell paper-with-code single-cell-omics scrna-seq-analysis reproducible-science single-cell-atac-seq reproducible-research
Created 2020-07-27
32 commits to master branch, last one about a year ago
theislab
scgen theislab
56
266
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
iSEE
iSEE iSEE
42
224
other
18
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
gui shiny clustering single-cell hacktoberfest visualization gene-expression transcriptomics human-cell-atlas feature-extraction dimension-reduction
Created 2017-12-06
3,242 commits to devel branch, last one about a month ago
ZJUFanLab
scCATCH ZJUFanLab
38
218
gpl-3.0
5
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
seurat rna-seq sequencing single-cell cell-markers marker-genes transcriptome transcriptomics cluster-annotation
Created 2019-08-06
118 commits to master branch, last one about a year ago
samuel-marsh
scCustomize samuel-marsh
24
218
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
nf-core
scrnaseq nf-core
172
214
mit
135
A single-cell RNAseq pipeline for 10X genomics data
alevin nf-core rna-seq bustools kallisto nextflow pipeline workflow star-solo cellranger 10xgenomics single-cell 10x-genomics
Created 2019-04-08
1,443 commits to master branch, last one 3 months ago