129 Open source projects that are alternatives of or similar to SPLiT-Seq_demultiplexing

Papers with code for single cell related papers

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

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

Simulating single-cell data using gene regulatory networks 📠

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

Single cell type annotation guided by cell atlases, with freedom to be queer

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

Clustering scRNAseq by genotypes

Harmony framework for connecting scRNA-seq data from discrete time points

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

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

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

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.

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

A collection of 50+ trajectory inference methods within a common interface 📥📤

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

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

Clone identification from single-cell data

Reference mapping for single-cell genomics

BEER: Batch EffEct Remover for single-cell data

A comprehensive dimensional reduction framework to recover the latent topology from high-dimensional data.

Fast and accurate sequence demultiplexing

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

A tool for semi-automatic cell type annotation

Reliable, scalable and demultiplexing for single-cell RNA sequencing. Improves genotypes with Expectation-Maximization

Discrete Distributional Differential Expression

Data-driven Network-based Bayesian Inference of Drivers

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.

Find causal cell-types underlying complex trait genetics

A simple tool to calculate reads number and total base count in FASTQ file

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

Frequently used commands in bioinformatics

No description or website provided.

Conversion between scRNA-seq objects

Metacell - Single-cell mRNA Analysis

Bioinformatics library in Kotlin

Methods for detecting doublets in single-cell sequencing data

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

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

mgatk: mitochondrial genome analysis toolkit

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

Single-cell Hierarchical Poisson Factorization

Examples using Clustergrammer2 to explore high-dimensional datasets.

Multiome GRN inference.

Reconstruction of complex single-cell trajectories using CellRouter

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

Community-provided extensions to Seurat

No description or website provided.

scLearn：Learning for single cell assignment

Efficient handling of FASTQ files from Python

Stacked Denoising AutoEncoder based on TensorFlow

Quantifying experimental perturbations at single cell resolution

R API and htmlwidget for Vitessce

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

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

Single-cell exploratory data analysis for RNA-Seq

Spatial Transcriptomics Dashboard

Nanopore demultiplexing, QC and alignment pipeline

spatial transcriptome, single cell

cTPnet Package