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Search results for rna seq single cell

57 search results found

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Single Cell Best Practices ⭐ 544

https://www.sc-best-practices.org

Single Cell Pseudotime ⭐ 367

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Scrna Tools ⭐ 295

Table of software for the analysis of single-cell RNA-seq data.

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

Youtubetutorials ⭐ 180

Sccatch ⭐ 171

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Dittoseq ⭐ 153

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

Single cell analysis in the browser

Scrnaseq ⭐ 119

A single-cell RNAseq pipeline for 10X genomics data

Alevin Fry ⭐ 115

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Powsimr ⭐ 102

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

Scrnaseqpipeline ⭐ 73

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

Single Cell Training ⭐ 63

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Covid 19 Rna Seq Datasets ⭐ 61

A repository for sharing information on available COVID-19 RNA-Seq datasets

Kallistobustools ⭐ 55

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Iterative transfer learning with neural network improves clustering and cell type classification in single-cell RNA-seq analysis

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Scribe Py ⭐ 36

Regulatory networks with Direct Information in python

BRIE: Bayesian Regression for Isoform Estimate in Single Cells

Spatialtranscriptomics ⭐ 34

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Next-Gen Sequencing tools from the Horvath Lab

Expressionmatrix2 ⭐ 27

Software for exploration of gene expression data from single-cell RNA sequencing.

Scib Reproducibility ⭐ 25

Additional code and analysis from the single-cell integration benchmarking project

ASAP : Automated Single-cell Analysis Pipeline

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

Beyondcell ⭐ 23

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments.

Popsicler ⭐ 22

popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.

Deepcycle ⭐ 19

Cell cycle inference in single-cell RNA-seq

Devcellpy ⭐ 18

devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing.

Rpanglaodb ⭐ 17

An R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database into a Seurat object.

Splatter Paper ⭐ 15

Data and analysis for the Splatter paper

Dropclust ⭐ 15

Version 2.1.0 released

Dynamical systems methods for RNA velocity analysis

Uncurl_python ⭐ 14

UNCURL is a tool for single cell RNA-seq data analysis.

Lr Splitpipe ⭐ 13

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

Bgeedb_r ⭐ 13

Source code of the R packge BgeeDB to use data from the Bgee database

Rna Combine ⭐ 11

RNA-seq data comprehensive data analysis toolbox

Couplednmf ⭐ 11

Coupled clustering of single cell genomic data

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

A Unified RNA Sequencing Model (URSM) for joint analysis of single cell and bulk RNA-seq data.

MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data

Fatecompass ⭐ 8

Maximum mean discrepancy comparisons for single cell profiling experiments

Trendcatcher ⭐ 7

TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255

Discotoolkit_py ⭐ 7

DISCO by Scientist for Scientist for You

Accurately annotating scRNA-seq data using two rounds of reference-based classification

Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:

Single Cell Genomes with Allele Specificity

Phd Thesis ⭐ 5

My PhD thesis - "Tools and techniques for single-cell RNA sequencing data"

Digitaldlsorter ⭐ 5

digitalDLSorteR: An R package to deconvolute bulk RNA-Seq using scRNA-Seq data

Genocraft ⭐ 5

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

Celltalkdb ⭐ 5

A manually curated database of literature-supported ligand-receptor interactions in human and mouse

This is a standalone interactive Shiny tool to analyze and explore single-cell RNA-seq data from human coronary artery.

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