Topic: single-cell Goto Github

👇 Here are 746 public repositories matching this topic...

aertslab / pyscenic
single-cell,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 regulatory networks and cell types from single-cell RNA-seq data.
Organization: aertslab
Home Page: http://scenic.aertslab.org
single-cell transcriptomics gene-regulatory-network transcription-factors

agitter / single-cell-pseudotime
single-cell,An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
User: agitter
single-cell rna-seq bioinformatics pseudotime-algorithms

bowang-lab / scgpt
single-cell,
Organization: bowang-lab
Home Page: https://scgpt.readthedocs.io/en/latest/
foundation-model gpt single-cell

broadinstitute / wot
single-cell,A software package for analyzing snapshots of developmental processes
Organization: broadinstitute
Home Page: https://broadinstitute.github.io/wot/
single-cell rna-seq time-series trajectory optimal-transport

cangermueller / deepcpg
single-cell,Deep neural networks for predicting CpG methylation
User: cangermueller
deep-neural-networks deeplearning methylation epigenetics single-cell

combine-lab / alevin-fry
single-cell,🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Organization: combine-lab
Home Page: https://alevin-fry.readthedocs.io
single-cell rust transcriptomics rna-seq single-cell-rna-seq quantification 10x

combine-lab / salmon
single-cell,🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Organization: combine-lab
Home Page: https://combine-lab.github.io/salmon
quasi-mapping bioinformatics rna-seq rnaseq salmon quantification sailfish c-plus-plus gene-expression scrna-seq

csn-le / wave_clus
single-cell,A fast and unsupervised algorithm for spike detection and sorting using wavelets and super-paramagnetic clustering
Organization: csn-le
spike-sorting neuroscience single-cell polytrodes

digitalcytometry / ecotyper
single-cell,EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
Organization: digitalcytometry
tumor microenvironment single-cell bulk-rna-seq deconvolution

dtm2451 / dittoseq
single-cell,Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
User: dtm2451
rna-seq single-cell single-cell-rna-seq visualization color-blindness color-blind

enblacar / scpubr
single-cell,Generate high quality, publication ready visualizations for single cell transcriptomics data.
User: enblacar
Home Page: https://enblacar.github.io/SCpubr-book/
data-visualization ggplot2 publication-quality-plots r rstats seurat single-cell-genomics single-cell-rna-seq visualization single-cell

flowhub-team / awesome-omics
single-cell,A collection of awesome things regarding all omics.
User: flowhub-team
genomics protein single-cell ngs ngs-pipeline wgs-analysis awesome omics

gao-lab / glue
single-cell,Graph-linked unified embedding for single-cell multi-omics data integration
Organization: gao-lab
bioinformatics deep-learning single-cell single-cell-multiomics

genecell / single-cell-papers-with-code
single-cell,Papers with code for single cell related papers
User: genecell
single-cell scrna-seq scrna-seq-analysis reproducible-research reproducible-science single-cell-omics single-cell-atac-seq paper-with-code

hemberg-lab / scrna.seq.datasets
single-cell,Collection of public scRNA-Seq datasets used by our group
Organization: hemberg-lab
Home Page: https://hemberg-lab.github.io/scRNA.seq.datasets/
docker dataset single-cell s3-storage jenkins aws openstack mkdocs

hms-dbmi / scde
single-cell,R package for analyzing single-cell RNA-seq data
Organization: hms-dbmi
Home Page: http://pklab.med.harvard.edu/scde
bioinformatics single-cell transcriptomics heterogenity analysis r ngs

immunomind / immunarch
single-cell,🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
Organization: immunomind
Home Page: https://immunarch.com
immunology tcr tcr-repertoire immunoinformatics immune-repertoire rep-seq bcr-repertoire bcr ig ig-repertoire

isee / isee
single-cell,R/shiny interface for interactive visualization of data in SummarizedExperiment objects
Organization: isee
Home Page: https://bioconductor.org/packages/iSEE/
visualization gui dimension-reduction feature-extraction clustering transcriptomics single-cell gene-expression shiny human-cell-atlas

juexinwang / scgnn
single-cell,scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks
User: juexinwang
single-cell scrna-seq-analysis graph-neural-network

kanaverse / kana
single-cell,Single cell analysis in the browser
Organization: kanaverse
Home Page: https://kanaverse.org/kana/
single-cell interactive-visualizations exploratory-data-analysis webassembly rna-seq cite-seq bioinformatics interactive-analysis

kharchenkolab / numbat
single-cell,Haplotype-aware CNV analysis from single-cell RNA-seq
Organization: kharchenkolab
Home Page: https://kharchenkolab.github.io/numbat/
cancer-genomics cnv-detection single-cell phylogeny single-cell-analysis single-cell-rna-seq spatial-transcriptomics lineage-tracing

kharchenkolab / pagoda2
single-cell,R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
Organization: kharchenkolab
single-cell transcriptomics scrna-seq single-cell-rna-seq

kpatel427 / youtubetutorials
single-cell,
User: kpatel427
bioinformatics bioinformatics-analysis rna-seq single-cell tutorials youtube

krishnaswamylab / phate
single-cell,PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
Organization: krishnaswamylab
Home Page: http://phate.readthedocs.io
single-cell dimensionality-reduction data-visualization unsupervised-learning manifold-learning

luntergroup / octopus
single-cell,Bayesian haplotype-based mutation calling
Organization: luntergroup
genomics variant-calling bioinformatics variants haplotypes somatic-variants de-novo-mutation phasing single-cell

mdozmorov / scrna-seq_notes
single-cell,A list of scRNA-seq analysis tools
User: mdozmorov
scrna-seq single-cell

milaboratory / mixcr
single-cell,MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
Organization: milaboratory
Home Page: https://mixcr.com
bioinformatics immunology antibody t-cell-receptor t-cell rep-seq 10x rna-seq sequencing single-cell

nf-core / scrnaseq
single-cell,A single-cell RNAseq pipeline for 10X genomics data
Organization: nf-core
Home Page: https://nf-co.re/scrnaseq
nf-core nextflow workflow pipeline 10x-genomics 10xgenomics alevin bustools cellranger kallisto

omicsml / dance
single-cell,DANCE: a deep learning library and benchmark platform for single-cell analysis
Organization: omicsml
Home Page: https://pydance.readthedocs.io
bioinformatics dance data-science deep-learning graph-neural-networks machine-learning multimodality python single-cell spatial-transcriptomics

plger / scdblfinder
single-cell,Methods for detecting doublets in single-cell sequencing data
User: plger
Home Page: https://plger.github.io/scDblFinder/
single-cell doublets

saezlab / decoupler-py
single-cell,Python package to perform enrichment analysis from omics data.
Organization: saezlab
Home Page: https://decoupler-py.readthedocs.io/
python data-science bioinformatics transcriptomics numba single-cell spatial-transcriptomics enrichment enrichment-analysis

saezlab / liana-py
single-cell,LIANA+: an all-in-one framework for cell-cell communication
Organization: saezlab
Home Page: http://liana-py.readthedocs.io/
cell-cell-communication ligand-receptor python single-cell single-cell-rna-seq spatial spatialomics

samuel-marsh / sccustomize
single-cell,R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
User: samuel-marsh
Home Page: https://samuel-marsh.github.io/scCustomize/
customization ggplot2 seurat single-cell single-cell-genomics single-cell-rna-seq visualization scrna-seq

scrna-tools / scrna-tools
single-cell,Table of software for the analysis of single-cell RNA-seq data.
Organization: scrna-tools
Home Page: https://www.scrna-tools.org
database rna-seq scrna-seq single-cell single-cell-rna-seq software tools

sdparekh / zumis
single-cell,zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
User: sdparekh
rnaseq rna-seq single-cell umi expression barcodes fastq dge pipeline

seandavi / awesome-single-cell
single-cell,Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
User: seandavi
rna-seq-data gene-expression scrna-seq-data bioinformatics awesome-list dimensionality-reduction cell-cycle atac-seq analysis cell-differentiation

single-cell-genetics / cellsnp-lite
single-cell,Efficient genotyping bi-allelic SNPs on single cells
Organization: single-cell-genetics
Home Page: https://cellsnp-lite.readthedocs.io
single-cell genetic-variants genotyping

starlitnightly / omicverse
single-cell,A python library for multi omics included bulk and single cell RNA-seq analysis.
User: starlitnightly
Home Page: https://omicverse.readthedocs.io/
bioinformatics omics bulk-rna-seq single-cell

stemangiola / tidyseurat
single-cell,Seurat meets tidyverse. The best of both worlds.
User: stemangiola
Home Page: https://stemangiola.github.io/tidyseurat/
tibble single-cell-rna-seq seurat tidyverse ggplot2 pca umap tsne single-cell dplyr

stuart-lab / signac
single-cell,R toolkit for the analysis of single-cell chromatin data
Organization: stuart-lab
Home Page: https://stuartlab.org/signac/
single-cell bioinformatics atac

tallulandrews / scrnaseqpipeline
single-cell,
User: tallulandrews
single-cell-rna-seq single-cell rna-seq

teichlab / celltypist
single-cell,A tool for semi-automatic cell type classification
Organization: teichlab
Home Page: https://www.celltypist.org/
python single-cell machine-learning scrna-seq cell-type-classification label-transfer

theislab / scarches
single-cell,Reference mapping for single-cell genomics
Organization: theislab
Home Page: https://docs.scarches.org/en/latest/
single-cell deep-learning rna-seq-analysis data-integration batch-correction multimodal-deep-learning multiomics single-cell-genomics scrna-seq human-cell-atlas

theislab / scgen
single-cell,Single cell perturbation prediction
Organization: theislab
Home Page: https://scgen.readthedocs.io
transcriptomics deep-learning generative-model bioinformatics single-cell scrna-seq single-cell-genomics

theislab / single-cell-best-practices
single-cell,https://www.sc-best-practices.org
Organization: theislab
Home Page: https://www.sc-best-practices.org
book rna-seq single-cell tutorial

velocyto-team / velocyto.py
single-cell,RNA velocity estimation in Python
Organization: velocyto-team
Home Page: http://velocyto.org/velocyto.py/
rna-velocity-estimation rna-seq single-cell

vitessce / vitessce
single-cell,Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
Organization: vitessce
Home Page: http://vitessce.io
gehlenborglab single-cell imaging hubmap kharchenkolab data-visualization vitessce hidivelab zarr

welch-lab / liger
single-cell,R package for integrating and analyzing multiple single-cell datasets
Organization: welch-lab
r single-cell nonnegative-matrix-factorization

zhanghao-njmu / scp
single-cell,An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
User: zhanghao-njmu
Home Page: https://zhanghao-njmu.github.io/SCP/
single-cell seurat-objects single-cell-analysis single-cell-rna-seq scrna-pipeline scrna-seq scrna-seq-analysis seurat scanpy anndata single-cell-omics single-cell-sequencing shiny-apps shiny-app shinyapps single-cell-atac-seq single-cell-genomics single-cell-pipeline scatac-seq

zjufanlab / sccatch
single-cell,Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
User: zjufanlab
Home Page: https://www.sciencedirect.com/science/article/pii/S2589004220300663
cell-markers cluster-annotation marker-genes rna-seq sequencing seurat single-cell transcriptome transcriptomics