Maintained elsewhere. See README.
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Updated
Mar 11, 2023 - C++
Maintained elsewhere. See README.
Prediction of surface protein expression from mRNA expression using a regression auto-encoder neural network.
adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data
Project analyzing multi-omics genomics data from a COVID-19 study.
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.
Awesome single-cell CITE-sequencing Pipeline
A ShinyApp for visualization and explorering Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data
experimental interface between R and scvi-tools
CITE-seq profiling of human PBMCs at baseline and activation conditions
MultiModal Classifier Hierarchy (MMoCHi)
Material for Bioconductor 2023 workshop on interoperation with python
A framework for simulation of spatially-resolved omics data using python
A single-cell demultiplexing pipeline, the sharp (♯)
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
Novel joint clustering method with scRNA-seq and CITE-seq data
Tools for single-cell feature barcoding analysis
Scripts related to bulkRNA-seq as well as single-cell CITE-seq and VDJ-seq data of Gearty et al. (2021)
scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
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