cite-seq

There are 29 repositories under cite-seq topic.

  • scverse/scvi-tools

    Deep probabilistic analysis of single-cell and spatial omics data

    Language:Python1.2k251k344

  • scverse/muon

    muon is a multimodal omics Python framework

    Language:Python2091410730

  • kanaverse/kana

    Single cell analysis in the browser

    Language:JavaScript141612012

  • 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)).

    Language:R120133419

  • sanderlab/scPerturb

    scPerturb: A resource and a python/R tool for single-cell perturbation data

    Language:Jupyter Notebook1025266

  • 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.

    Language:Python9256212

  • alexisvdb/singleCellHaystack

    Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

    Language:R78589

  • niaid/dsb

    Normalize CITEseq Data

    Language:R63104313

  • Novartis/scar

    scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics

    Language:Python488194

  • yezhengSTAT/ADTnorm

    ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.

    Language:R20594

  • AlexsLemonade/scpca-nf

    scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

    Language:R1253592

  • 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.

    Language:R116230

  • Terkild/CITE-seq_optimization

    Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments

    Language:R9202
  • MMoCHi

    donnafarberlab/MMoCHi

    MultiModal Classifier Hierarchy (MMoCHi)

    Language:Python6122

  • tarot0410/BREMSC

    Novel joint clustering method with scRNA-seq and CITE-seq data

    Language:R6113

  • vjcitn/scviR

    experimental interface between R and scvi-tools

    Language:R6210

  • abcwcm/GeartySchietinger

    Scripts related to bulkRNA-seq as well as single-cell CITE-seq and VDJ-seq data of Gearty et al. (2021)

    Language:HTML5014

  • jlduan/fba

    Tools for single-cell feature barcoding analysis

    Language:Python5113

  • nlawlor/PBMC_CITEseq

    CITE-seq profiling of human PBMCs at baseline and activation conditions

    Language:R5211

  • hisplan/sharp

    A single-cell demultiplexing pipeline, the sharp (♯)

    Language:Jupyter Notebook4201

  • SylviaYZ/bios-611-project

    Project analyzing multi-omics genomics data from a COVID-19 study.

    Language:R4100

  • OpenOmics/cyte-seek

    Awesome single-cell CITE-sequencing Pipeline

    Language:Python2110

  • pinellolab/simstpy

    A framework for simulation of spatially-resolved omics data using python

    Language:Jupyter Notebook2101

  • JulianSpagnuolo/adtseq

    adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data

    Language:C++1100

  • yuan-yin-truly/peanutX

    Maintained elsewhere. See README.

    Language:C++1100

  • zqzneptune/ShinyCITExpresso

    A ShinyApp for visualization and explorering Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data

    Language:R1100

  • 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

    Language:HTML0100

  • karthik-d/rna-protein-autoencoder

    Prediction of surface protein expression from mRNA expression using a regression auto-encoder neural network.

    Language:Python20

  • vjcitn/BiocPyInterop

    Material for Bioconductor 2023 workshop on interoperation with python

    Language:R201