Topic: single-cell-rna-seq Goto Github

👇 Here are 372 public repositories matching this topic...

bcgsc / rna-bloom
single-cell-rna-seq,:hibiscus: reference-free transcriptome assembly for short and long reads
Organization: bcgsc
denovo-assembly rna-seq single-cell-rna-seq bioinformatics-tool nanopore-sequencing bulk-rna-seq pacbio-sequencing

bioconductor / orchestratingsinglecellanalysis
single-cell-rna-seq,Content for the OSCA Book.
Organization: bioconductor
Home Page: http://bioconductor.org/books/devel/OSCA/
book book-base single-cell rna-seq single-cell-rna-seq

cole-trapnell-lab / monocle3
single-cell-rna-seq,
Organization: cole-trapnell-lab
single-cell-rna-seq

combine-lab / alevin-fry
single-cell-rna-seq,🐟 🔬🦀 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-rna-seq,🐟 🍣 🍱 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

dtm2451 / dittoseq
single-cell-rna-seq,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

dynverse / dynmethods
single-cell-rna-seq,A collection of 50+ trajectory inference methods within a common interface 📥📤
Organization: dynverse
Home Page: https://dynverse.org
single-cell-rna-seq single-cell-analysis bioinformatics-algorithms trajectory-inference-methods trajectory-inference pseudotemporal-ordering

dynverse / dynverse
single-cell-rna-seq,A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
Organization: dynverse
Home Page: http://dynverse.org
trajectory-inference-methods benchmarking single-cell-rna-seq single-cell-omics single-cell scrna-seq

enblacar / scpubr
single-cell-rna-seq,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

gao-lab / cell_blast
single-cell-rna-seq,A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
Organization: gao-lab
Home Page: http://cblast.gao-lab.org
deep-learning single-cell-rna-seq bioinformatics single-cell

gregoryschwartz / too-many-cells
single-cell-rna-seq,Cluster single cells and analyze cell clade relationships with colorful visualizations.
User: gregoryschwartz
Home Page: https://gregoryschwartz.github.io/too-many-cells/
single-cell visualization single-cell-analysis single-cell-rna-seq bioinformatics-pipeline bioinformatics-algorithms

hemberg-lab / sc3
single-cell-rna-seq,A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
Organization: hemberg-lab
Home Page: http://bioconductor.org/packages/SC3
bioconductor-package human-cell-atlas single-cell-rna-seq

hemberg-lab / scmap
single-cell-rna-seq,A tool for unsupervised projection of single cell RNA-seq data
Organization: hemberg-lab
Home Page: http://bioconductor.org/packages/scmap
single-cell-rna-seq projection-mapping r bioconductor-package human-cell-atlas

jefworks-lab / honeybadger
single-cell-rna-seq,HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
Organization: jefworks-lab
Home Page: http://jef.works/HoneyBADGER/
single-cell-analysis single-cell-rna-seq cnv-detection transcriptomics subpopulation hmm bayesian heterogeneity bioinformatics

kevinmenden / scaden
single-cell-rna-seq,Deep Learning based cell composition analysis with Scaden.
User: kevinmenden
Home Page: https://scaden.readthedocs.io
deep-learning deconvolution bioinformatics single-cell-rna-seq rna-seq cell-composition-analysis machine-learning

kharchenkolab / conos
single-cell-rna-seq,R package for the joint analysis of multiple single-cell RNA-seq datasets
Organization: kharchenkolab
scrna-seq single-cell-rna-seq batch-correction

kharchenkolab / dropest
single-cell-rna-seq,Pipeline for initial analysis of droplet-based single-cell RNA-seq data
Organization: kharchenkolab
pipeline preprocessing scrna-seq single-cell-rna-seq

kharchenkolab / numbat
single-cell-rna-seq,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-rna-seq,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

martinjzhang / scdrs
single-cell-rna-seq,Single-cell disease relevance score (scDRS)
User: martinjzhang
Home Page: https://martinjzhang.github.io/scDRS/
cell-state diseases-and-complex-traits gwas single-cell-rna-seq within-cell-type-heterogeneity

mojaveazure / seurat-disk
single-cell-rna-seq,Interfaces for HDF5-based Single Cell File Formats
User: mojaveazure
Home Page: https://mojaveazure.github.io/seurat-disk
single-cell-rna-seq single-cell-genomics hdf5-format

nunofonseca / irap
single-cell-rna-seq,integrated RNA-seq Analysis Pipeline
User: nunofonseca
bulk-rna-seq differential-expression exon-quantification gene-expression irap pipeline rna-seq rna-seq-analysis single-cell-rna-seq transcript-quantification

omicsml / dance
single-cell-rna-seq,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

pachterlab / kb_python
single-cell-rna-seq,A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
Organization: pachterlab
Home Page: https://www.kallistobus.tools/
bustools kallisto single-cell-rna-seq rna-velocity-estimation scrna-seq kb-python

parashardhapola / scarf
single-cell-rna-seq,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.
User: parashardhapola
Home Page: http://scarf.readthedocs.io
big-data bioinformatics cite-seq clustering differential-expression dimension-reduction gene-modules genomics graph-analytics memory-efficient multiomics pseudotime scalable-data-analysis scatac-seq scrna-seq single-cell-atac-seq single-cell-genomics single-cell-rna-seq tsne umap

quadbio / scrnaseq_analysis_vignette
single-cell-rna-seq,Tutorial for scRNA-seq data analysis beginners using R
Organization: quadbio
bioinformatics single-cell-analysis single-cell-rna-seq tutorial

rnabioco / clustifyr
single-cell-rna-seq,Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
Organization: rnabioco
Home Page: https://rnabioco.github.io/clustifyr/
rna-seq clusters marker-genes assign-identities single-cell-rna-seq

saeyslab / multinichenetr
single-cell-rna-seq,MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Organization: saeyslab
cell-cell-communication differential-expression intercellular-communication intercellular-signaling ligand-receptor ligand-receptor-interaction ligand-target scrna-seq single-cell single-cell-rna-seq

saeyslab / nichenetr
single-cell-rna-seq,NicheNet: predict active ligand-target links between interacting cells
Organization: saeyslab
single-cell-omics intercellular-communication ligand-receptor ligand-target data-integration single-cell-rna-seq rna-seq gene-expression network-inference cell-cell-communication

saezlab / liana-py
single-cell-rna-seq,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-rna-seq,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

satijalab / azimuth
single-cell-rna-seq,A Shiny web app for mapping datasets using Seurat v4
Organization: satijalab
Home Page: https://satijalab.org/azimuth
shiny-app single-cell-genomics single-cell-rna-seq

satijalab / seurat
single-cell-rna-seq,R toolkit for single cell genomics
Organization: satijalab
Home Page: http://www.satijalab.org/seurat
cran human-cell-atlas single-cell-genomics single-cell-rna-seq

sccaf / sccaf
single-cell-rna-seq,Single-Cell Clustering Assessment Framework
Organization: sccaf
single-cell-rna-seq clustering-algorithm machine-learning

scrna-tools / scrna-tools
single-cell-rna-seq,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

scverse / scvi-tools
single-cell-rna-seq,Deep probabilistic analysis of single-cell and spatial omics data
Organization: scverse
Home Page: http://scvi-tools.org/
scrna-seq variational-bayes variational-autoencoder cite-seq single-cell-genomics single-cell-rna-seq deep-generative-model human-cell-atlas scverse deep-learning

scverse / squidpy
single-cell-rna-seq,Spatial Single Cell Analysis in Python
Organization: scverse
Home Page: https://squidpy.readthedocs.io/en/stable/
single-cell-rna-seq single-cell-genomics spatial-transcriptomics spatial-analysis image-analysis data-visualization squidpy

stemangiola / tidyseurat
single-cell-rna-seq,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

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

tanaylab / metacell
single-cell-rna-seq,Metacell - Single-cell mRNA Analysis
Organization: tanaylab
Home Page: https://tanaylab.github.io/metacell
single-cell-rna-seq

theislab / cellrank
single-cell-rna-seq,CellRank: dynamics from multi-view single-cell data
Organization: theislab
Home Page: https://cellrank.org
machine-learning single-cell-rna-seq bioinformatics rna-velocity markov-chains genetics data-science fuzzy-clustering-analyses manifold-learning single-cell-genomics

theislab / cpa
single-cell-rna-seq,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, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
Organization: theislab
single-cell-genomics single-cell-rna-seq scrna-seq human-cell-atlas

theislab / diffxpy
single-cell-rna-seq,Differential expression analysis for single-cell RNA-seq data.
Organization: theislab
Home Page: https://diffxpy.rtfd.io
differential-expression single-cell-rna-seq gene-set-enrichment bioinformatics transcriptomics tensorflow

theislab / sccoda
single-cell-rna-seq,A Bayesian model for compositional single-cell data analysis
Organization: theislab
tensorflow compositional-changes statistical-analysis single-cell-rna-seq

ttgump / scdeepcluster
single-cell-rna-seq,scDeepCluster for Single Cell RNA-seq data
User: ttgump
single-cell-rna-seq deep-learning unsupervised-learning

vivianstats / scimpute
single-cell-rna-seq,Accurate and robust imputation of scRNA-seq data
User: vivianstats
Home Page: https://www.nature.com/articles/s41467-018-03405-7
imputation single-cell-rna-seq r-package

xuranw / music
single-cell-rna-seq,Multi-subject Single Cell Deconvolution
User: xuranw
Home Page: https://github.com/xuranw/MuSiC
single-cell-rna-seq statistical-genetics

yanwu2014 / swne
single-cell-rna-seq,Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
User: yanwu2014
single-cell-rna-seq single-cell-analysis data-visualization dimensionality-reduction nonnegative-matrix-factorization bioinformatics single-cell-genomics statistical-methods single-cell-atac-seq

yoseflab / cassiopeia
single-cell-rna-seq,A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
Organization: yoseflab
Home Page: https://cassiopeia-lineage.readthedocs.io/en/latest/
single-cell-rna-seq lineage-tracing single-cell-lineage-tracing computational-phylogenetics computational-biology crispr-cas9

zhanghao-njmu / scp
single-cell-rna-seq,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/
anndata scanpy scatac-seq scrna-pipeline scrna-seq scrna-seq-analysis seurat seurat-objects shiny-app shiny-apps shinyapps single-cell single-cell-analysis single-cell-atac-seq single-cell-genomics single-cell-omics single-cell-pipeline single-cell-rna-seq single-cell-sequencing