Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Other scRNA-seq data analysis tools

A A A
NMFEM
Desktop

NMFEM

Analyzes a wide variety of scRNA-Seq datasets, ranging from mouse hematopoietic…

Analyzes a wide variety of scRNA-Seq datasets, ranging from mouse hematopoietic stem cells to human glioblastoma data. NMFEM generates protein-protein interaction (PPI) network modules from selected…

A A A
scRNASeqDB
Dataset

scRNASeqDB

Collects and curates gene expression profiles of the transcriptome of human…

Collects and curates gene expression profiles of the transcriptome of human single cells. scRNASeqDB provides various features such as gene expression in different cell types, expression patterns at…

A A A
Worm Single…
Desktop

Worm Single Cell

Infers signalling networks at cellular level for cell fate specification based…

Infers signalling networks at cellular level for cell fate specification based on multiple data types, including single-cell gene expression data, PPI data, PDI data and Genetic Interaction (GI)…

A A A
DECODE
Algorithm

DECODE

Identifies functionally relevant pairs of genes that are complementary to…

Identifies functionally relevant pairs of genes that are complementary to others measures. DECODE determines the extent of joint presence or absence of genes across different cells. This algorithm…

G T A T C G C T A
SIDR
Desktop

SIDR Simultaneous Isolation of genomic DNA and total RNA

Provides a method for the simultaneous isolation of genomic DNA and total RNA…

Provides a method for the simultaneous isolation of genomic DNA and total RNA from single cells. SIDR physically isolates total RNA, regardless of polyadenylation, from the single-cell lysate that…

A A A
scploid
Desktop

scploid Single Cell RNA-seq Aneuploidy Caller

Provides an approach for aneuploidies calling in single-cell RNA-sequencing.…

Provides an approach for aneuploidies calling in single-cell RNA-sequencing. scploid is an R package performing for each cell, the identification of chromosomes including genes with potentially…

A A A
WagnerEtAl2017
Algorithm

WagnerEtAl2017

Provides an effective algorithm for smoothing single-cell RNA-Seq data. This…

Provides an effective algorithm for smoothing single-cell RNA-Seq data. This method combines a previously proposed normalization method with a standard variance-stabilizing transformation (VST) for…

A A A
pseudodynamics
Desktop

pseudodynamics

Allows users to understand population growth and differentiation…

Allows users to understand population growth and differentiation characteristics along trajectories. pseudodynamics simplifies the integration of wildtype and mutant data to annotate developmental…

A A A
mcSCRB-seq
Desktop

mcSCRB-seq molecular crowding Single-Cell RNA-Barcoding and Sequencing

Improves the sensitivity and efficiency of Single-Cell RNA-Barconding and…

Improves the sensitivity and efficiency of Single-Cell RNA-Barconding and Sequencing (SCRB-seq). mcSCRB-seq is a highly flexible, fast and efficient library protocol with low set-up costs and hence…

A A A
PerraudeauEtAl2…
Desktop

PerraudeauEtAl2017

Permits downstream analysis. This tool contains four steps: (1) dimensionality…

Permits downstream analysis. This tool contains four steps: (1) dimensionality reduction accounting for zero inflation and over-dispersion, and adjusting for gene and cell-level covariates; (2)…

A A A
VAMF
Desktop

VAMF Varying-censoring Aware Matrix Factorization

Allows to model cell-specific detection patterns using random effects. VAMF…

Allows to model cell-specific detection patterns using random effects. VAMF helps users to identify the factors in the case of systematic bias. This tool represents a probabilistic dimension…

A A A
scImpute
Desktop

scImpute

Address the dropout events prevalent in scRNAseq data. scImpute is an…

Address the dropout events prevalent in scRNAseq data. scImpute is an imputation method that determines which values are affected by dropout events in data and performs imputation only on dropout…

A A A
UBiT2
Web
Desktop

UBiT2 User-friendly BioInformatics Tools

Provides installation-free, offline alignment, analysis, and visualization of…

Provides installation-free, offline alignment, analysis, and visualization of RNA-sequencing as well as qPCR data. UBiT2 can perform gene set enrichment testing by using the non-parametric minimal…

A A A
WemIQ
Desktop

WemIQ Weighted-log-likelihood expectation maximization method on Isoform Quantification

Integrates an effective bias removal with a weighted expectation maximization…

Integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads among isoforms efficiently. WemIQ improves the quantification of isoform and gene…

A A A
Kinetics of…
Desktop

Kinetics of transcription

A statistical framework for studying the kinetics of stochastic gene expression…

A statistical framework for studying the kinetics of stochastic gene expression from single-cell RNA-seq data. The proposed statistical model provides a flexible and efficient way to investigate the…

ROMA
Desktop

ROMA Representation Of Module Activity

Approximates the expression data of a gene set by its first principal…

Approximates the expression data of a gene set by its first principal component. ROMA is based on the simplest uni-factor linear model of gene regulation. It addresses the issue of quantifying the…

A A A
schimera
Desktop

schimera

Tackles the polymerase chain reaction chimera problem in scRNA-seq by filtering…

Tackles the polymerase chain reaction chimera problem in scRNA-seq by filtering molecules that, for a given cell barcode and unique molecular identifier pair, have low read abundance.

A A A
PlateEffects201…
Desktop

PlateEffects2016

A package for the summation of counts across all cells on each plate for each…

A package for the summation of counts across all cells on each plate for each gene. The count sums can then be used in a differentially expressed (DE) analysis, effectively treating plates as…

A A A
scPLS
Desktop

scPLS

A statistical method that solves a key challenge in data normalization for…

A statistical method that solves a key challenge in data normalization for single cell RNA sequencing: controlling for the hidden confounding factors (e.g. batch effects, cell cycle effects etc.) and…

A A A
Sphinx
Desktop

Sphinx

Improves the detection of changes in the transcriptional heterogeneity pattern…

Improves the detection of changes in the transcriptional heterogeneity pattern of in single-cell RNA-seq data using two heterogeneity parameters: "burst proportion" and "burst…

A A A
SciBrow
Web

SciBrow

Provides an interactive web-browser environment for the visualization of single…

Provides an interactive web-browser environment for the visualization of single cell genomics. SciBrow was developed to detect contamination of DNA contig scaffolds. It uses principal component…

A A A
SingleCellExper…
Desktop

SingleCellExperiment

Defines a S4 class for storing data from single-cell experiments.…

Defines a S4 class for storing data from single-cell experiments. SingleCellExperiment is an R package that includes specialized methods to store and retrieve spike-in information, dimensionality…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.