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scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution Nature

Hybrid BAG-seq: DNA and RNA from the same single nucleus reveals interactions between genomic and transcriptomic landscapes in human tumor samples Genome Biology

Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq Science | AAAS

Illumina Single Cell 3' RNA Prep Kits | Scalable scRNA-Seq library prep Illumina

Protocol for isolating the single bacteriocyte from whiteflies for single-cell RNA-seq analysis ScienceDirect.com

Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing Nature

scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration Genome Biology

Stereo-cell: Spatial enhanced-resolution single-cell sequencing with high-density DNA nanoball-patterned arrays Science | AAAS

SWIFT-seq enables comprehensive single-cell transcriptomic profiling of circulating tumor cells in multiple myeloma and its precursors Nature

Long-read RNA sequencing of transposable elements from single cells using CELLO-seq Nature

Single-cell transcriptomic and genomic changes in the ageing human brain Nature

Application of RNA-seq for single nucleotide variation identification in a cohort of patients with hypertrophic cardiomyopathy Nature

snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues Nature

Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics Nature

Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state Nature

Feature selection methods affect the performance of scRNA-seq data integration and querying Nature

Simultaneous single-cell DNA damage profiling and RNA sequencing by Paired-Damage-seq Nature

UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing Nature

Decoding heterogeneous single-cell perturbation responses Nature

Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations Nature

Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq ScienceDirect.com

Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2 Science | AAAS

HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling Genome Biology

Single-cell RNA-seq reveals immune cell heterogeneity and increased Th17 cells in human fibrotic skin diseases Frontiers

Highly effective batch effect correction method for RNA-seq count data ScienceDirect.com

Label-free single-cell RNA multiplexing leveraging genetic variability Nature

LGC Biosearch Technologies launches Amp-Seq One SelectScience

scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors Science | AAAS

Live-seq enables temporal transcriptomic recording of single cells Nature

Single-cell RNA sequencing PacBio

Holo-Seq: single-cell sequencing of holo-transcriptome Genome Biology

Microfluidics-free single-cell genomics with templated emulsification Nature

SCITO-seq: single-cell combinatorial indexed cytometry sequencing Nature

LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis Genome Biology

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons Science | AAAS

txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility Genome Biology

scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics Genome Biology

Single-cell nascent RNA sequencing unveils coordinated global transcription Nature

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin ScienceDirect.com

High-throughput total RNA sequencing in single cells using VASA-seq Nature

SMOOTH-seq: single-cell genome sequencing of human cells on a third-generation sequencing platform Genome Biology

Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison BMC Genomics

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq ScienceDirect.com

scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells Genome Biology

Functional analysis of structural variants in single cells using Strand-seq Nature

Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq Nature

scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing Genome Biology

Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection Nature

CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential Nature

epiAneufinder identifies copy number alterations from single-cell ATAC-seq data Nature

Systematic evaluation of single-cell RNA-seq analyses performance based on long-read sequencing platforms ScienceDirect.com

Comparison of transformations for single-cell RNA-seq data Nature

Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq Nature

The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves ScienceDirect.com

Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq ScienceDirect.com

TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing Nature

snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives Nature

scID Uses Discriminant Analysis to Identify Transcriptionally Equivalent Cell Types across Single-Cell RNA-Seq Data with Batch Effect ScienceDirect.com

scTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs Nature

Prime-seq, efficient and powerful bulk RNA sequencing Genome Biology

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems ScienceDirect.com

A mapping in vivo using picoMeRIP–seq Nature

SEC-seq: association of molecular signatures with antibody secretion in thousands of single human plasma cells Nature

scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells ScienceDirect.com

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis Frontiers

scChIX-seq infers dynamic relationships between histone modifications in single cells Nature

A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation ScienceDirect.com

Inference of single-cell network using mutual information for scRNA-seq data analysis BMC Bioinformatics

One Cell At a Time (OCAT): a unified framework to integrate and analyze single-cell RNA-seq data Genome Biology

Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace Nature

Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications BioMed Central

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors Nature

QTL-Seq and Sequence Assembly Rapidly Mapped the Gene BrMYBL2.1 for the Purple Trait in Brassica rapa Nature

Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq Science | AAAS

AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data Genome Biology

Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling Nature

A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data Genome Biology

Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis Genome Biology

sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human adipose tissues ScienceDirect.com

DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide Nature

Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis ScienceDirect.com

Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq Nature

From bulk, single-cell to spatial RNA sequencing Nature

Single-nucleotide variant calling in single-cell sequencing data with Monopogen Nature

Cellcano: supervised cell type identification for single cell ATAC-seq data Nature

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis Genome Biology

Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging Nature

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants Genome Biology

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain Nature

Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus Science | AAAS

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding Nature

INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing Genome Biology

Analyzing genomic and epigenetic profiles in single cells by hybrid transposase (scGET-seq) ScienceDirect.com

Integrated Single Cell and Bulk RNA-Seq Analysis Revealed Immunomodulatory Effects of Ulinastatin in Sepsis: A Multicenter Cohort Study Frontiers

Genotype-free demultiplexing of pooled single-cell RNA-seq Genome Biology

Single-cell RNA-seq mapping of chicken peripheral blood leukocytes BMC Genomics

Improved Bacterial Single-Cell RNA-Seq through Automated MATQ-Seq and Cas9-Based Removal of rRNA Reads ASM Journals

Scalable genetic screening for regulatory circuits using compressed Perturb-seq Nature

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome Science | AAAS

FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells Frontiers