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Flow cytometry analysis workflow. The aim of this project is to provide an intuitive workflow for the analysis of high-dimensionality cytometry data in R.

R 11 2 Updated Jan 23, 2025

Reproducibility repository accompanying Wilk, Lee, Wei, Parks, et al. "Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19" bioRxiv (2020).

R 3 3 Updated Jul 14, 2021

Methods to compute Local Inverse Simpson's Index (LISI)

R 60 5 Updated Sep 2, 2021

Java tools for analyzing Drop-seq data

Java 124 35 Updated Jan 21, 2025

A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.

R 101 44 Updated Nov 22, 2022

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

R 225 42 Updated Dec 10, 2024

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)

HTML 281 99 Updated Jul 28, 2020

RNA-seq workflow using STAR and DESeq2

Python 333 206 Updated Aug 1, 2024

A tool that allows to get UMI counts from a single cell protein assay

Python 79 43 Updated Jul 22, 2024

Scripts and Snakemake pipeline used in the EMBL-ABR webinar

13 4 Updated Jul 24, 2019

Near-optimal RNA-Seq quantification

C 672 173 Updated Dec 3, 2024

A SingleCell RNASeq pre-processing snakemake workflow

Python 146 47 Updated Jan 11, 2023

Read trimming tool for Illumina NGS data.

Java 130 90 Updated Mar 10, 2015

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

3,281 999 Updated Dec 4, 2024

Differential expression analysis for single-cell RNA-seq data.

Python 195 23 Updated May 30, 2023

Single-cell analysis in Python. Scales to >1M cells.

Python 1,982 610 Updated Jan 24, 2025
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