71 Open source projects that are alternatives of or similar to scPower

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

Single-Cell Omics Preparation Entity Tools

Discrete Distributional Differential Expression

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

Single cell analysis in the browser

spatial transcriptome, single cell

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

Make rapid visualizations of RNA-seq data in R

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

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

Single-cell copy number calling and event history reconstruction.

No description or website provided.

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Reference mapping for single-cell genomics

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

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Graph-linked unified embedding for single-cell multi-omics data integration

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Efficient genotyping bi-allelic SNPs on single cells

Methods for detecting doublets in single-cell sequencing data

Convert between AnnData and SingleCellExperiment

Manuscript for functional prediction of transcriptomic “dark matter” across species

Conditional out-of-distribution prediction

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

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

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

Interactive visualizations for differential expression

Inference of switch-like differential expression along single-cell trajectories

A tool for semi-automatic cell type annotation

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

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

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

Porting DESeq2 and DEXSeq into python via rpy2

Bead-based single-cell atac processing

Dynamical systems methods for RNA velocity analysis

CUT&RUN and CUT&Tag data processing and analysis

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

Tools for single-cell data processing

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

mgatk: mitochondrial genome analysis toolkit

Mouse cell atlas

Compare different differential abundance and expression methods

R package to visualize gene expression data based on weighted kernel density estimation

Multiome GRN inference.

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

Papers with code for single cell related papers

Fit generalized linear models in python.

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Shiny app and R package to perform a power analysis to select the number of participants in intensive longitudinal studies

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

R API and htmlwidget for Vitessce