cite-seq

There are 0 repository under cite-seq topic.

scverse / scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
scrna-seq variational-bayes variational-autoencoder cite-seq single-cell-genomics single-cell-rna-seq deep-generative-model human-cell-atlas scverse deep-learning
Language:Python 1125
scverse / muon
muon is a multimodal omics Python framework
multimodal-data multimodal-omics-analysis multi-omics anndata scanpy mudata muon scrna-seq scatac-seq cite-seq scverse
Language:Python 196
kanaverse / kana
Single cell analysis in the browser
single-cell interactive-visualizations exploratory-data-analysis webassembly rna-seq cite-seq bioinformatics interactive-analysis
Language:JavaScript 131
rezakj / iCellR
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)).
singel-cell-sequencing clustering-algorithm clustering normalization umap pseudotime scrna-seq scvdj-seq cite-seq 3d intractive-graph 10xgenomics dropout batch-normalization imputation diffusion-maps cell-type-classification icellr
Language:R 116
parashardhapola / scarf
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.
bioinformatics single-cell-genomics single-cell-rna-seq dimension-reduction clustering umap tsne big-data cite-seq single-cell-atac-seq memory-efficient scalable-data-analysis scrna-seq scatac-seq pseudotime multiomics gene-modules differential-expression graph-analytics genomics
Language:Python 89
sanderlab / scPerturb
scPerturb: A resource and a python/R tool for single-cell perturbation data
cite-seq database perturbation scatac-seq science scrna-seq single-cell python r statistics
Language:Jupyter Notebook 87
alexisvdb / singleCellHaystack
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
bioinformatics single-cell r transcriptomics spatial-transcriptomics cite-seq pseudotime scatac-seq spatial-proteomics
Language:R 70
niaid / dsb
Normalize CITEseq Data
cite-seq niaid-tsang-lab
Language:R 59
Novartis / scar
scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
machine-learning single-cell-rna-seq denoising-algorithm variational-autoencoder probabilistic-graphical-models generative-model cite-seq crispr-screen pytorch
Language:Python 42
yezhengSTAT / ADTnorm
ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.
cite-seq data-integration single-cell surface-protein-normalization
Language:R 12
AlexsLemonade / scpca-nf
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
10xgenomics alevin-fry nextflow rna-seq-quantification scrna-seq cite-seq spatial-transcriptomics
Language:R 11
Terkild / CITE-seq_optimization
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
cite-seq single-cell-rna-seq single-cell-omics single-cell-proteomics antibody cytometry
Language:R 9
MMoCHi
donnafarberlab / MMoCHi
MultiModal Classifier Hierarchy (MMoCHi)
annotation cite-seq classification multimodal scrna-seq systems-biology
Language:Python 6
epigen / scrnaseq_processing_seurat
A Snakemake workflow for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.
bioinformatics workflow snakemake scrna-seq biomedical-data-science cite-seq sccrispr-seq 10xgenomics snrna-seq single-cell visualization
Language:R 6
tarot0410 / BREMSC
Novel joint clustering method with scRNA-seq and CITE-seq data
scrna-seq-analysis clustering-methods cite-seq
Language:R 6
vjcitn / scviR
experimental interface between R and scvi-tools
bioconductor cite-seq scverse
Language:R 6
abcwcm / GeartySchietinger
Scripts related to bulkRNA-seq as well as single-cell CITE-seq and VDJ-seq data of Gearty et al. (2021)
single-cell rna-seq cite-seq tcr-repertoire
Language:HTML 4
jlduan / fba
Tools for single-cell feature barcoding analysis
feature-barcodes targeted-transcripts cell-partitioning cell-hashing crispr cite-seq cellplex multi-seq eccite-seq phage-atac single-cell
Language:Python 4
nlawlor / PBMC_CITEseq
CITE-seq profiling of human PBMCs at baseline and activation conditions
shiny pbmc lps baseline anti-cd3 anti-cd28 single-cell-rna-seq cell-hashing cite-seq human-cell-atlas czi chan-zuckerberg-initiative immune-system single-cell visualization
Language:R 4
SylviaYZ / bios-611-project
Project analyzing multi-omics genomics data from a COVID-19 study.
bioinformatics cite-seq multiomics scrna-seq covid-19
Language:R 4
hisplan / sharp
A single-cell demultiplexing pipeline, the sharp (♯)
hashtag cite-seq cell-hashing asap-seq cellplex
Language:Jupyter Notebook 3
OpenOmics / cyte-seek
Awesome single-cell CITE-sequencing Pipeline
pipeline singularity single-cell cite-seq quality-control 10xgenomics
Language:Python 2
pinellolab / simstpy
A framework for simulation of spatially-resolved omics data using python
atac-seq cite-seq cut-tag-seq multi-omics rna-seq simulation spatial
Language:Jupyter Notebook 2
JulianSpagnuolo / adtseq
adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data
citeseq cite-seq dropseqtools dropseq drop-seq 10x 10x-genomics scrna-seq scrna-seq-analysis scrnaseq
Language:C++ 1
yuan-yin-truly / peanutX
Maintained elsewhere. See README.
bayesian-hierarchical-model cite-seq decontamination single-cell
Language:C++ 1
zqzneptune / ShinyCITExpresso
A ShinyApp for visualization and explorering Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data
cite-seq multiomics r shiny-apps
Language:R 1
razofz / DB_AKC_citeseq
Accompanying code for analysis of manuscript in Nature Aging: Implications of stress-induced gene expression for hematopoietic stem cell aging studies
bioinformatics cite-seq jupyter multiome quarto rna-seq
Language:HTML 0
karthik-d / rna-protein-autoencoder
Prediction of surface protein expression from mRNA expression using a regression auto-encoder neural network.
autoencoder autoencoder-neural-network cite-seq mrna protein-expression pytorch single-cell-analysis torch fine-tuning protein-rna-interactions regression-model
Language:Python
vjcitn / BiocPyInterop
Material for Bioconductor 2023 workshop on interoperation with python
basilisk bioconductor cite-seq genetics hail reticulate scvi-tools single-cell-omics spark
Language:R

cite-seq

scverse / scvi-tools

scverse / muon

kanaverse / kana

rezakj / iCellR

parashardhapola / scarf

sanderlab / scPerturb

alexisvdb / singleCellHaystack

niaid / dsb

Novartis / scar

yezhengSTAT / ADTnorm

AlexsLemonade / scpca-nf

Terkild / CITE-seq_optimization

donnafarberlab / MMoCHi

epigen / scrnaseq_processing_seurat

tarot0410 / BREMSC

vjcitn / scviR

abcwcm / GeartySchietinger

jlduan / fba

nlawlor / PBMC_CITEseq

SylviaYZ / bios-611-project

hisplan / sharp

OpenOmics / cyte-seek

pinellolab / simstpy

JulianSpagnuolo / adtseq

yuan-yin-truly / peanutX

zqzneptune / ShinyCITExpresso

razofz / DB_AKC_citeseq

karthik-d / rna-protein-autoencoder

vjcitn / BiocPyInterop