Topic: scrna-seq Goto Github

👇 Here are 360 public repositories matching this topic...

antoniodefalco / scevan
scrna-seq,R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
User: antoniodefalco
Home Page: https://www.nature.com/articles/s41467-023-36790-9
single-cell copy-number-variation copynumber subclonal-deconvolution subclone-identification clonal-evolution clonal-analysis microenvironment tumor-heterogeneity tumor-classification

aristoteleo / dynamo-release
scrna-seq,Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
Organization: aristoteleo
Home Page: https://dynamo-release.readthedocs.io/en/latest/
dynamo scslam-seq scrna-seq vector-field potential-landscape nasc-seq sci-fate scnt-seq rna-velocity cell-fate

broadinstitute / tangram
scrna-seq,Spatial alignment of single cell transcriptomic data.
Organization: broadinstitute
spatial-data visium gene-expression scrna-seq snrna-seq computational-biology

catavallejos / basics
scrna-seq,BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
User: catavallejos
bayesian single-cell scrna-seq r rcpp rcpparmadillo gene-expression bioconductor-package

changwn / scfea
scrna-seq,single cell Flux Estimation Analysis (scFEA) Try the below web server!
User: changwn
Home Page: http://scflux.org/
single-cell metabolism scrna-seq metabolic-modules

chanzuckerberg / cellxgene
scrna-seq,An interactive explorer for single-cell transcriptomics data
Organization: chanzuckerberg
Home Page: https://chanzuckerberg.github.io/cellxgene/
scientific visualization scrna-seq transcriptomics dataviz

combine-lab / salmon
scrna-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

czbiohub-sf / cerebra
scrna-seq,A tool for fast and accurate summarizing of variant calling format (VCF) files
Organization: czbiohub-sf
variant-calling mutations scrna-seq genomics

danko-lab / ted
scrna-seq,a fully Bayesian approach to deconvolve tumor microenvironment
Organization: danko-lab
scrna-seq bulk-rna-seq tumor-cells stromal-cells expression-profile tumor-expression deconvolution

dpeerlab / palantir
scrna-seq,Single cell trajectory detection
Organization: dpeerlab
Home Page: https://palantir.readthedocs.io
scrna-seq scrna-seq-analysis manifold-learning dimensionality-reduction diffusion-maps markov-chain differentiation single-cell-genomics trajectory-generation cell-fate-transitions

dynverse / dynverse
scrna-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

eleozzr / desc
scrna-seq,Deep Embedding for Single-cell Clustering
User: eleozzr
Home Page: https://eleozzr.github.io/desc/
desc batch-remove scrna-seq deep-learning clustering

genecell / single-cell-papers-with-code
scrna-seq,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

immunogenomics / harmony
scrna-seq,Fast, sensitive and accurate integration of single-cell data with Harmony
Organization: immunogenomics
Home Page: https://portals.broadinstitute.org/harmony/
scrna-seq algorithm data-integration r

immunogenomics / symphony
scrna-seq,Efficient and precise single-cell reference atlas mapping with Symphony
Organization: immunogenomics
r scrna-seq bioinfo mapping

interactivereport / cellxgene_vip
scrna-seq,Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
User: interactivereport
Home Page: https://cellxgenevip-ms.bxgenomics.com
scrna-seq cellxgene scanpy visualization seurat svg publication-quality-plots cellxgene-vip

jonathanshor / doubletdetection
scrna-seq,Doublet detection in single-cell RNA-seq data.
User: jonathanshor
Home Page: https://doubletdetection.readthedocs.io/en/stable/
scrna-seq

junjunlab / scrnatoolvis
scrna-seq,Useful functions to make your scRNA-seq plot more cool!
User: junjunlab
scrna-seq visualization elegant yyds

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

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

klugerlab / alra
scrna-seq,Imputation method for scRNA-seq based on low-rank approximation
Organization: klugerlab
scrna-seq svd imputation dropout matrix-completion

lilab-bcb / cirrocumulus
scrna-seq,Bring your single-cell data to life
Organization: lilab-bcb
Home Page: https://cirrocumulus.readthedocs.io/
scrna-seq visualization single-cell anndata bioinformatics transcriptomics webgl scanpy seurat spatial

liulab-dfci / maestro
scrna-seq,Single-cell Transcriptome and Regulome Analysis Pipeline
User: liulab-dfci
scatac-seq scrna-seq epigenetics snakemake-workflows transcription-factors gene-regulatory-networks

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

oshlack / splatter
scrna-seq,Simple simulation of single-cell RNA sequencing data
Organization: oshlack
bioconductor simulation scrna-seq bioinformatics

pachterlab / kb_python
scrna-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
scrna-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
bioinformatics single-cell-genomics single-cell-rna-seq dimension-reduction clustering umap tsne big-data cite-seq single-cell-atac-seq

paulingliu / rogue
scrna-seq,Assessing the purity of single cell population
User: paulingliu
quantification scrna-seq purity clustering

pinellolab / stream
scrna-seq,STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
Organization: pinellolab
Home Page: http://stream.pinellolab.org
singlecell trajectory lineage visualization scatac-seq scrna-seq python

rezakj / icellr
scrna-seq,Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
User: rezakj
singel-cell-sequencing clustering-algorithm clustering normalization umap pseudotime scrna-seq scvdj-seq cite-seq 3d

saeyslab / multinichenetr
scrna-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

samuel-marsh / sccustomize
scrna-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

sanderlab / scperturb
scrna-seq,scPerturb: A resource and a python/R tool for single-cell perturbation data
Organization: sanderlab
Home Page: http://www.sanderlab.org/scPerturb/
cite-seq database perturbation python r scatac-seq science scrna-seq single-cell statistics

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

scverse / muon
scrna-seq,muon is a multimodal omics Python framework
Organization: scverse
Home Page: https://muon.scverse.org/
multimodal-data multimodal-omics-analysis multi-omics anndata scanpy mudata muon scrna-seq scatac-seq cite-seq

scverse / scvi-tools
scrna-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

simslab / schpf
scrna-seq,Single-cell Hierarchical Poisson Factorization
Organization: simslab
scrna-seq dimensionality-reduction variational-bayes

single-cell-genetics / vireo
scrna-seq,Demultiplexing pooled scRNA-seq data with or without genotype reference
Organization: single-cell-genetics
Home Page: https://vireoSNP.readthedocs.io
single-cells scrna-seq demultiplex donor-deconvolution variational-inference

teichlab / cellhint
scrna-seq,A tool for semi-automatic cell type harmonization and integration
Organization: teichlab
cell-type-harmonization data-integration machine-learning python scrna-seq single-cell

teichlab / celltypist
scrna-seq,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 / cpa
scrna-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 / scarches
scrna-seq,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
scrna-seq,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 / zellkonverter
scrna-seq,Conversion between scRNA-seq objects
Organization: theislab
Home Page: https://theislab.github.io/zellkonverter/
scrna-seq r conversion bioconductor

vandijklab / cell2sentence-ft
scrna-seq,Cell2Sentence turns scRNA-seq data into text for LLM training.
Organization: vandijklab
bioinformatics scrna-seq scrna-seq-data single-cell

wheaton5 / souporcell
scrna-seq,Clustering scRNAseq by genotypes
User: wheaton5
scrna-seq scrnaseq scrna-seq-analysis bioinformatics computational-biology genomics

zhanghao-njmu / scp
scrna-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/
single-cell seurat-objects single-cell-analysis single-cell-rna-seq scrna-pipeline scrna-seq scrna-seq-analysis seurat scanpy anndata

zjufanlab / bulk2space
scrna-seq,a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles
User: zjufanlab
bulk-sequencing deep-learning scrna-seq spatial-transcriptomics

zjufanlab / scdeepsort
scrna-seq,Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
User: zjufanlab
Home Page: https://doi.org/10.1093/nar/gkab775
annotation cell-type-classification deep-learning gnn graph-neural-network reference-free scrna-seq single-cell transcriptomics