(Q64071552)

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

Europe PubMed Central

22 June 2022

https://europepmc.org/article/PMC/6460256

inferred from PubMed Central ID database lookup

DESeq2

object named as

DESeq2

DEseq2

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

DESeq2

0 references

cites work

Functions and mechanisms of RNA editing

1 reference

12 December 2020

Proposed methods for testing and selecting the ERCC external RNA controls

1 reference

12 December 2020

Alternative isoform regulation in human tissue transcriptomes

1 reference

12 December 2020

WGCNA: an R package for weighted correlation network analysis

1 reference

12 December 2020

mRNA-Seq whole-transcriptome analysis of a single cell

1 reference

12 December 2020

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

1 reference

12 December 2020

A scaling normalization method for differential expression analysis of RNA-seq data

1 reference

12 December 2020

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

1 reference

12 December 2020

A survey of sequence alignment algorithms for next-generation sequencing

1 reference

12 December 2020

Tackling the widespread and critical impact of batch effects in high-throughput data

1 reference

12 December 2020

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

1 reference

12 December 2020

Computational methods for transcriptome annotation and quantification using RNA-seq

1 reference

12 December 2020

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

1 reference

12 December 2020

Overview of available methods for diverse RNA-Seq data analyses

1 reference

12 December 2020

Highly multiplexed and strand-specific single-cell RNA 5' end sequencing.

1 reference

12 December 2020

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

1 reference

12 December 2020

CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification

1 reference

12 December 2020

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.

1 reference

12 December 2020

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

1 reference

12 December 2020

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

1 reference

12 December 2020

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

1 reference

12 December 2020

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.

1 reference

12 December 2020

Accounting for technical noise in single-cell RNA-seq experiments.

1 reference

12 December 2020

Systematic evaluation of spliced alignment programs for RNA-seq data

1 reference

12 December 2020

Quantitative single-cell RNA-seq with unique molecular identifiers

1 reference

12 December 2020

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells

1 reference

12 December 2020

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

1 reference

12 December 2020

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

1 reference

12 December 2020

Bayesian approach to single-cell differential expression analysis

1 reference

12 December 2020

Normalization of RNA-seq data using factor analysis of control genes or samples

1 reference

12 December 2020

svaseq: removing batch effects and other unwanted noise from sequencing data

1 reference

12 December 2020

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

1 reference

12 December 2020

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

1 reference

12 December 2020

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

1 reference

12 December 2020

limma powers differential expression analyses for RNA-sequencing and microarray studies

1 reference

12 December 2020

Computational and analytical challenges in single-cell transcriptomics

1 reference

12 December 2020

Expression profiling. Combinatorial labeling of single cells for gene expression cytometry

1 reference

12 December 2020

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

1 reference

12 December 2020

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

1 reference

12 December 2020

Ballgown bridges the gap between transcriptome assembly and expression analysis

1 reference

12 December 2020

HISAT: a fast spliced aligner with low memory requirements

1 reference

12 December 2020

Identification of cell types from single-cell transcriptomes using a novel clustering method.

1 reference

12 December 2020

Spatial reconstruction of single-cell gene expression data

1 reference

12 December 2020

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

1 reference

12 December 2020

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

1 reference

12 December 2020

The technology and biology of single-cell RNA sequencing

1 reference

12 December 2020

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

1 reference

12 December 2020

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.

1 reference

12 December 2020

Technologies for Single-Cell Isolation

1 reference

12 December 2020

ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer

1 reference

12 December 2020

Single-cell messenger RNA sequencing reveals rare intestinal cell types

1 reference

12 December 2020

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

1 reference

12 December 2020

Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes

1 reference

12 December 2020

Mapping RNA-seq Reads with STAR

1 reference

12 December 2020

ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis

1 reference

12 December 2020

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

1 reference

12 December 2020

Unique features of long non-coding RNA biogenesis and function

1 reference

12 December 2020

destiny: diffusion maps for large-scale single-cell data in R.

1 reference

12 December 2020

Robust detection of alternative splicing in a population of single cells

1 reference

12 December 2020

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

1 reference

12 December 2020

Classification of low quality cells from single-cell RNA-seq data

1 reference

12 December 2020

Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data

1 reference

12 December 2020

pcaReduce: hierarchical clustering of single cell transcriptional profiles

1 reference

12 December 2020

Design and computational analysis of single-cell RNA-sequencing experiments

1 reference

12 December 2020

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

1 reference

12 December 2020

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq

1 reference

12 December 2020

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

1 reference

12 December 2020

Wishbone identifies bifurcating developmental trajectories from single-cell data

1 reference

12 December 2020

Quality control of single-cell RNA-seq by SinQC.

1 reference

12 December 2020

Beta-Poisson model for single-cell RNA-seq data analyses

1 reference

12 December 2020

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

1 reference

12 December 2020

Circular RNAs: analysis, expression and potential functions

1 reference

12 December 2020

Characterizing and annotating the genome using RNA-seq data

1 reference

12 December 2020

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

1 reference

12 December 2020

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

1 reference

12 December 2020

Single-cell RNA-sequencing: The future of genome biology is now

1 reference

12 December 2020

Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation

1 reference

12 December 2020

Diffusion pseudotime robustly reconstructs lineage branching.

1 reference

12 December 2020

Identifying and annotating human bifunctional RNAs reveals their versatile functions

1 reference

12 December 2020

Loss of RNA expression and allele-specific expression associated with congenital heart disease.

1 reference

12 December 2020

Single Cell Isolation and Analysis

1 reference

12 December 2020

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

1 reference

12 December 2020

Massively parallel digital transcriptional profiling of single cells

1 reference

12 December 2020

Effective detection of variation in single-cell transcriptomes using MATQ-seq.

1 reference

12 December 2020

Single-cell mRNA quantification and differential analysis with Census

1 reference

12 December 2020

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

1 reference

12 December 2020

Comparative Analysis of Single-Cell RNA Sequencing Methods.

1 reference

12 December 2020

Power analysis of single-cell RNA-sequencing experiments

1 reference

12 December 2020

SC3: consensus clustering of single-cell RNA-seq data

1 reference

12 December 2020

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

1 reference

12 December 2020

SCnorm: robust normalization of single-cell RNA-seq data

1 reference

12 December 2020

SCALE: modeling allele-specific gene expression by single-cell RNA sequencing.

1 reference

12 December 2020

Normalizing single-cell RNA sequencing data: challenges and opportunities

1 reference

12 December 2020

BRIE: transcriptome-wide splicing quantification in single cells

1 reference

12 December 2020

Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation

1 reference

12 December 2020

Identifying cell populations with scRNASeq.

1 reference

12 December 2020

Comprehensive single-cell transcriptional profiling of a multicellular organism.

1 reference

12 December 2020

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

1 reference

12 December 2020

Massively parallel single-nucleus RNA-seq with DroNc-seq

1 reference

12 December 2020

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

1 reference

12 December 2020

Circular RNAs in cancer: opportunities and challenges in the field.

1 reference

12 December 2020

SCENIC: single-cell regulatory network inference and clustering.

1 reference

12 December 2020

Missing data and technical variability in single-cell RNA-sequencing experiments

1 reference

12 December 2020

Bias, robustness and scalability in single-cell differential expression analysis

1 reference

12 December 2020

Reconstruction of complex single-cell trajectories using CellRouter.

1 reference

12 December 2020

An accurate and robust imputation method scImpute for single-cell RNA-seq data.

1 reference

12 December 2020

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.

1 reference

12 December 2020

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.

1 reference

12 December 2020

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

1 reference

12 December 2020

Using single-cell genomics to understand developmental processes and cell fate decisions.

1 reference

12 December 2020

DEsingle for detecting three types of differential expression in single-cell RNA-seq data.

1 reference

12 December 2020

BCseq: accurate single cell RNA-seq quantification with bias correction.

1 reference

12 December 2020

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.

1 reference

12 December 2020

DrImpute: imputing dropout events in single cell RNA sequencing data.

1 reference

12 December 2020

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

1 reference

12 December 2020

SAVER: gene expression recovery for single-cell RNA sequencing.

1 reference

12 December 2020

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

1 reference

12 December 2020

Comparison of computational methods for imputing single-cell RNA-sequencing data

1 reference

12 December 2020

Single-cell RNA sequencing technologies and bioinformatics pipelines

1 reference

12 December 2020

AutoImpute: Autoencoder based imputation of single-cell RNA-seq data

1 reference

12 December 2020

Dimensionality reduction for visualizing single-cell data using UMAP

1 reference

12 December 2020

GrandPrix: scaling up the Bayesian GPLVM for single-cell data

1 reference

12 December 2020

A test metric for assessing single-cell RNA-seq batch correction

1 reference

12 December 2020

M3Drop: dropout-based feature selection for scRNASeq

1 reference

12 December 2020