Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
☆55Feb 15, 2021Updated 5 years ago
Alternatives and similar repositories for scRNA-seq-pipelines
Users that are interested in scRNA-seq-pipelines are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially ex…☆107Aug 1, 2023Updated 2 years ago
- An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.☆37Mar 15, 2023Updated 3 years ago
- R markdown notebooks for the Tabula Muris network analysis in Iacono et al. (2019)☆12Jun 30, 2021Updated 4 years ago
- ☆46May 17, 2022Updated 3 years ago
- Comparison of dimensionality reduction methods☆30Mar 24, 2020Updated 6 years ago
- Collection of useful methods for single cell analysis☆15Aug 22, 2024Updated last year
- Analysis code for the TAP-seq manuscript.☆11Jun 25, 2021Updated 4 years ago
- This repository contains HCA Benchmarking codes☆26Nov 11, 2019Updated 6 years ago
- pipelines to process scRNA-seq data☆12Jan 11, 2021Updated 5 years ago
- General notes and resources on how to analyze Spatial Transcriptomics data☆12Jun 20, 2023Updated 2 years ago
- ☆56Dec 13, 2020Updated 5 years ago
- Tumor-Infiltrating CD8 Lymphocytes states prediction☆14Feb 7, 2024Updated 2 years ago
- benchmark for single-cell RNA-seq imputation methods☆29Mar 16, 2024Updated 2 years ago
- Multi-sample multi-group scRNA-seq analysis tools☆221Mar 8, 2026Updated 2 weeks ago
- Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data☆109Jul 3, 2023Updated 2 years ago
- Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and S…☆44Nov 25, 2024Updated last year
- single cell and bulk RNASeq analysis scripts☆14Jan 13, 2022Updated 4 years ago
- ☆16Dec 11, 2018Updated 7 years ago
- Client to access ExperimentHub resources☆11Oct 30, 2025Updated 4 months ago
- R package to identify genes with differential distributions in single-cell RNA-seq☆34Mar 24, 2022Updated 3 years ago
- Interfaces for HDF5-based Single Cell File Formats☆175Nov 4, 2023Updated 2 years ago
- iSEE repository for the Shiny contest☆13Mar 15, 2020Updated 6 years ago
- List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.☆14Sep 3, 2016Updated 9 years ago
- zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs☆291Jul 12, 2024Updated last year
- Tools and methods for analysis of single cell assay data in R☆262Oct 17, 2025Updated 5 months ago
- Comparison of single cell normalization strategies☆10Aug 13, 2021Updated 4 years ago
- SHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection☆17Apr 26, 2021Updated 4 years ago
- Single-Cell Clustering Assessment Framework☆108Oct 27, 2023Updated 2 years ago
- Survival Analysis for Protein-Level TCGA Analysis☆11Nov 30, 2018Updated 7 years ago
- Clone of the Bioconductor repository for the scRNAseq package.☆29Oct 10, 2025Updated 5 months ago
- A Bayesian model for compositional single-cell data analysis☆193Jan 13, 2026Updated 2 months ago
- Downstream analysis script for sci-fate (TF-gene linkage analysis / cell linkage analysis)☆24Jan 22, 2020Updated 6 years ago
- Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)☆16Jun 28, 2025Updated 8 months ago
- Algorithm for the inference of cell types from single-cell RNA-seq data.☆47May 13, 2016Updated 9 years ago
- Here I show how to use Deep Autoencoders for single cell RNA sequencing data analysis☆19May 5, 2019Updated 6 years ago
- Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)☆19May 6, 2019Updated 6 years ago
- cfDNA Sequencing Pipeline with UMI☆11Dec 8, 2025Updated 3 months ago
- A repository of case studies using ProjecTILs☆15Jul 26, 2024Updated last year
- SingleCellFusion--a tool to integrate single-cell transcriptome and epigenome data☆12Mar 13, 2022Updated 4 years ago