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Search results for r scrna seq

47 search results found

Scrna Seq_notes ⭐ 478

A list of scRNA-seq analysis tools

Harmony ⭐ 460

Fast, sensitive and accurate integration of single-cell data with Harmony

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Splatter ⭐ 195

Simple simulation of single-cell RNA sequencing data

Scrnatoolvis ⭐ 169

Useful functions to make your scRNA-seq plot more cool!

Sccustomize ⭐ 142

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

Zellkonverter ⭐ 112

Conversion between scRNA-seq objects

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

Interactive 3d Plotting In Seurat 3.0.0 ⭐ 88

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

Symphony ⭐ 73

Efficient and precise single-cell reference atlas mapping with Symphony

Dynverse ⭐ 58

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

Scperturb ⭐ 56

scPerturb: A resource and a python/R tool for single-cell perturbation data

Imputation method for scRNA-seq based on low-rank approximation

Cellpypes ⭐ 48

Cell type pipes for R

Scclusteval ⭐ 45

Single Cell Cluster Evaluation

Scclustviz ⭐ 42

Explore and share your scRNAseq clustering results

Discover differential transcript usage from polyA-captured single cell RNA-seq data

Scrna Recom ⭐ 36

collected resource for scRNA-seq analysis

A portable and fast single cell type identifier

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

R package IReNA

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.

scGSVA: Perform GSVA for single cell RNA seq

Accurate and fast cell marker gene identification with COSG

Cellrouter ⭐ 19

Reconstruction of complex single-cell trajectories using CellRouter

Cell type matching in single-cell RNA-sequencing data using FR-Match

BEER: Batch EffEct Remover for single-cell data

R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.

R package for analysing single cell data

Mudataseurat ⭐ 14

.h5mu files interface for Seurat

Robustsinglecell ⭐ 13

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.

The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data

Bgeedb_r ⭐ 13

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

Assessing the purity of single cell population

SHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection

Scpca Nf ⭐ 11

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

Clustermole ⭐ 11

Unbiased single-cell transcriptomic data cell type identification

Compartmap ⭐ 10

Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq

Apackoftheclones ⭐ 10

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.

Tmexplorer ⭐ 9

A collection of tumour microenvironment single-cell RNA sequencing datasets for use in R and other pipelines.

Reference-free celltype and phenotype annotation in single cell RNAseq by learning geneset representations

Normalization for single cell RNA-seq data

Simulation Comparison ⭐ 7

Snakemake workflow to benchmark scRNA-seq data simulators

1000 Tools Paper ⭐ 6

Code and analysis for the 1000 tools paper

Dea_seurat ⭐ 6

A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.

Single Cell RNA-seq UMI Filtering Facilitator

cross-species analysis of cell identities, markers and regulations

Dropletqc ⭐ 5

Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data

Intercellular communication analysis for scRNA-seq data

power analysis for scRNA-seq

IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis

Iscb2022_tidytranscriptomics ⭐ 5

Tidy Transcriptomics for Single-cell RNA Sequencing Analyses

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